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(-) Description

Title :  X-RAY STRUCTURE OF PENTAMERIC HIV-1 CA
 
Authors :  O. Pornillos
Date :  27 Sep 10  (Deposition) - 12 Jan 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pornillos, B. K. Ganser-Pornillos, M. Yeager
Atomic-Level Modelling Of The Hiv Capsid.
Nature V. 469 424 2011
PubMed-ID: 21248851  |  Reference-DOI: 10.1038/NATURE09640

(-) Compounds

Molecule 1 - HIV-1 CA
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 133-363
    GeneCA, GAG
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    StrainNL4-3

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1IOD10Ligand/IonIODIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS E:170 , ARG E:173BINDING SITE FOR RESIDUE IOD E 232
2AC2SOFTWAREARG A:162 , GLN A:219 , MET B:144BINDING SITE FOR RESIDUE IOD A 233
3AC3SOFTWAREGLU A:35 , LYS A:170 , ARG A:173 , GLN B:63BINDING SITE FOR RESIDUE IOD A 234
4AC4SOFTWARELYS B:170 , ARG B:173 , GLN C:63BINDING SITE FOR RESIDUE IOD B 232
5AC5SOFTWAREGLU C:35 , LYS C:170 , ARG C:173BINDING SITE FOR RESIDUE IOD C 232
6AC6SOFTWARELYS A:203 , LEU D:151BINDING SITE FOR RESIDUE IOD D 232
7AC7SOFTWAREGLU D:35 , LYS D:170BINDING SITE FOR RESIDUE IOD D 233
8AC8SOFTWAREGLU A:71 , GLU E:212BINDING SITE FOR RESIDUE IOD A 235
9AC9SOFTWAREPRO E:157 , LYS E:158 , GLU E:159BINDING SITE FOR RESIDUE IOD E 233

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:21 -E:22
2A:22 -B:21
3B:22 -C:21
4C:22 -D:21
5D:22 -E:21

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:121 -Pro A:122
2Asn B:121 -Pro B:122
3Asn C:121 -Pro C:122
4Asn D:121 -Pro D:122
5Asn E:121 -Pro E:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P05)

(-) Exons   (0, 0)

(no "Exon" information available for 3P05)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:210
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
            POL_HV1N5   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3         p05a1 A:1-147 automated matches                                                                                                         d3p05a2 A:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------....hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 A   1 PI---------HQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                             |       - |      20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                             2        12                                                                                                                                                                                                               

Chain A from PDB  Type:PROTEIN  Length:210
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
         Q72497_9HIV1   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3         p05a1 A:1-147 automated matches                                                                                                         d3p05a2 A:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------....hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 A   1 PI---------HQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                             |       - |      20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                             2        12                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
            POL_HV1N5   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05b1 B:1-147 automated matches                                                                                                                  d3p05b2 B:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 B   1 PIVQNLQGQMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                                               85         96                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
         Q72497_9HIV1   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05b1 B:1-147 automated matches                                                                                                                  d3p05b2 B:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 B   1 PIVQNLQGQMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                                               85         96                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
            POL_HV1N5   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05c1 C:1-147 automated matches                                                                                                                  d3p05c2 C:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 C   1 PIVQNLQGQMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                                               85         96                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
         Q72497_9HIV1   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05c1 C:1-147 automated matches                                                                                                                  d3p05c2 C:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 C   1 PIVQNLQGQMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                                               85         96                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:206
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
            POL_HV1N5   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05   d1 D:1-147 automated matches                                                                                                               ------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..---..ee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 D   1 PIVQN---QMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                |   10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                5   9                                                                          85         96                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:206
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
         Q72497_9HIV1   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3p05   d1 D:1-147 automated matches                                                                                                               ------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..---..ee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.----------....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 D   1 PIVQN---QMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP----------MREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                |   10        20        30        40        50        60        70        80    |    -     | 100       110       120       130       140       150       160       170       180       190       200       210         
                                5   9                                                                          85         96                                                                                                                           

Chain E from PDB  Type:PROTEIN  Length:199
 aligned with POL_HV1N5 | P12497 from UniProtKB/Swiss-Prot  Length:1435

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
            POL_HV1N5   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3         p05e1 E:1-147 automated matches                                                                                                         d3p05e2 E:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --         -----Gag_p24-3p05E01 E:17-219                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) --         -----Gag_p24-3p05E02 E:17-219                                                                                                                                                                                    Pfam domains (2)
           Pfam domains (3) --         -----Gag_p24-3p05E03 E:17-219                                                                                                                                                                                    Pfam domains (3)
           Pfam domains (4) --         -----Gag_p24-3p05E04 E:17-219                                                                                                                                                                                    Pfam domains (4)
           Pfam domains (5) --         -----Gag_p24-3p05E05 E:17-219                                                                                                                                                                                    Pfam domains (5)
         Sec.struct. author ..---------....hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.-----------...hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 E   1 PI---------HQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP-----------REPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                             |       - |      20        30        40        50        60        70        80    |    -      |100       110       120       130       140       150       160       170       180       190       200       210         
                             2        12                                                                       85          97                                                                                                                          

Chain E from PDB  Type:PROTEIN  Length:199
 aligned with Q72497_9HIV1 | Q72497 from UniProtKB/TrEMBL  Length:500

    Alignment length:219
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
         Q72497_9HIV1   133 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQ 351
               SCOP domains d3         p05e1 E:1-147 automated matches                                                                                                         d3p05e2 E:148-219 automated matches                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --         -----Gag_p24-3p05E01 E:17-219                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) --         -----Gag_p24-3p05E02 E:17-219                                                                                                                                                                                    Pfam domains (2)
           Pfam domains (3) --         -----Gag_p24-3p05E03 E:17-219                                                                                                                                                                                    Pfam domains (3)
           Pfam domains (4) --         -----Gag_p24-3p05E04 E:17-219                                                                                                                                                                                    Pfam domains (4)
           Pfam domains (5) --         -----Gag_p24-3p05E05 E:17-219                                                                                                                                                                                    Pfam domains (5)
         Sec.struct. author ..---------....hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.-----------...hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p05 E   1 PI---------HQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHP-----------REPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                             |       - |      20        30        40        50        60        70        80    |    -      |100       110       120       130       140       150       160       170       180       190       200       210         
                             2        12                                                                       85          97                                                                                                                          

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 9)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P05)

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit

(-) Gene Ontology  (50, 63)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (POL_HV1N5 | P12497)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004533    exoribonuclease H activity    Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oligonucleotides in both 5' to 3' and 3' to 5' directions.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0072494    host multivesicular body    A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain A,B,C,D,E   (Q72497_9HIV1 | Q72497)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POL_HV1N5 | P124971a43 1a8o 1afv 1ak4 1aum 1b92 1b9d 1b9f 1baj 1bhl 1bi4 1bis 1biu 1biz 1bl3 1gwp 1hiw 1hyv 1hyz 1itg 1k6y 1m9d 1qs4 1uph 1wjb 1wjd 1wkn 1za9 2b4j 2gol 2gon 2h3f 2h3i 2h3q 2h3v 2h3z 2hmx 2hvp 2itg 2jpr 2jyg 2jyl 2lf4 2lya 2lyb 2m3z 2m8l 2m8n 2m8p 2ont 2pwm 2pwo 2pxr 2x2d 2xde 2xv6 2xxm 3av9 3ava 3avb 3avc 3avf 3avg 3avh 3avi 3avj 3avk 3avl 3avm 3avn 3dik 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 3gv2 3h47 3h4e 3l3u 3l3v 3lpt 3lpu 3lry 3mge 3nf6 3nf7 3nf8 3nf9 3nfa 3p0a 3s85 3wne 3wnf 3wng 3wnh 4ah9 4ahr 4ahs 4aht 4ahu 4ahv 4coc 4cop 4dga 4dge 4dmn 4e1m 4e1n 4e91 4e92 4gvm 4gw6 4id1 4ipy 4jlh 4jmu 4lqw 4nx4 4o0j 4o55 4o5b 4phv 4qnb 4wym 4zhr 5hvp 9hvp
        Q72497_9HIV1 | Q724971m9d 2buo 2jmg 2lf4 2nv3 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 4dga 4dge
UniProtKB/TrEMBL
        Q72497_9HIV1 | Q724971l6n 1m9c 1m9e 1m9f 1m9x 1m9y 3obu 3obx 3p0a 5i4t 5mcz 5md0 5md1 5md2 5md3 5md4 5md5 5md6 5md7 5md8 5md9 5mda 5mdb 5mdc 5mdd 5mde 5mdf 5mdg

(-) Related Entries Specified in the PDB File

2dik CRYOEM-BASED MODEL OF CA HEXAMER
3gv2 STRUCTURE OF CA HEXAMER
3h47 STRUCTURE OF CA HEXAMER
3h4e STRUCTURE OF CA HEXAMER
3p0a