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(-) Description

Title :  HEXAMERIC HIV-1 CA, OPEN CONFORMATION
 
Authors :  A. J. Price, D. A. Jacques, L. C. James
Date :  08 Jan 16  (Deposition) - 10 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Capsid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Jacques, W. A. Mcewan, L. Hilditch, A. J. Price, G. J. Towers, L. C. James
Hiv-1 Uses Dynamic Capsid Pores To Import Nucleotides And Fuel Encapsidated Dna Synthesis.
Nature V. 536 349 2016
PubMed-ID: 27509857  |  Reference-DOI: 10.1038/NATURE19098

(-) Compounds

Molecule 1 - CAPSID PROTEIN P24
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAG
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: PR55GAG

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
11B06Ligand/IonN-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:53 , ASN A:57 , GLN A:63 , MET A:66 , LYS A:70 , TYR A:130 , ARG F:173binding site for residue 1B0 A 301
2AC2SOFTWARESER A:178 , GLN A:179 , GLU A:180 , ASN B:53 , ASN B:57 , GLN B:63 , MET B:66 , LYS B:70 , TYR B:130binding site for residue 1B0 B 301
3AC3SOFTWAREARG A:18 , ARG B:18binding site for residue CL B 302
4AC4SOFTWAREARG B:173 , ASN C:53 , LEU C:56 , ASN C:57 , GLN C:63 , MET C:66 , LYS C:70 , THR C:107 , TYR C:130binding site for residue 1B0 C 301
5AC5SOFTWAREARG C:173 , ASN D:53 , ASN D:57 , GLN D:63 , MET D:66 , LYS D:70 , THR D:107 , TYR D:130binding site for residue 1B0 D 301
6AC6SOFTWAREARG D:173 , ASN E:53 , LEU E:56 , ASN E:57 , GLN E:63 , MET E:66 , LYS E:70 , THR E:107 , TYR E:130binding site for residue 1B0 E 301
7AC7SOFTWAREARG E:173 , ASN F:53 , LEU F:56 , ASN F:57 , GLN F:63 , MET F:66 , LYS F:70 , TYR F:130binding site for residue 1B0 F 301

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:14 -F:45
2A:45 -B:14
3A:198 -A:218
4B:45 -C:14
5B:198 -B:218
6C:45 -D:14
7C:198 -C:218
8D:45 -E:14
9D:198 -D:218
10E:45 -F:14
11E:198 -E:218
12F:198 -F:218

(-) Cis Peptide Bonds  (6, 6)

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
6Asn F:121 -Pro F:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HGL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HGL)

(-) Exons   (0, 0)

(no "Exon" information available for 5HGL)

(-) 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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl A   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80      ||98       108       118       128       138       148       158       168       178 ||    192       202       212       
                                                                                                                 87|                                                                                 180|                                  
                                                                                                                  96                                                                                  185                                  


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh......hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl B   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAETETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80      ||99       109       119       129       139       149       159       169     ||189       199       209       219
                                                                                                                 87|                                                                           175|                                 
                                                                                                                  97                                                                            186                                 


Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl C   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAETETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80      ||98       108       118       128       138       148       158       168      |188       198       208       218 
                                                                                                                 87|                                                                            175|                                 
                                                                                                                  96                                                                             186                                 


Chain D from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl D   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAETETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80      ||98       108       118       128       138       148       158       168      |188       198       208       218 
                                                                                                                 87|                                                                            175|                                 
                                                                                                                  96                                                                             186                                 


Chain E from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl E   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80      ||98       108       118       128       138       148       158       168      |189       199       209       219
                                                                                                                 87|                                                                            175|                                
                                                                                                                  96                                                                             187                                


Chain F from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hgl F   1 PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEAATETLLVQNANPDCKTILKALGPGATLEEMMTACQ 219
                                    10        20        30        40        50        60        70        80    || 101       111       121       131       141       151       161       171   ||  189       199       209       219
                                                                                                               85|                                                                           175|                                   
                                                                                                                97                                                                            184
   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  (0, 0)

(no "SCOP Domain" information available for 5HGL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HGL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HGL)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hgl
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  GAG_HV1N5 | P12493
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV1N5 | P12493: 1gwp 1hiw 1uph 2c55 2x2d 3gv2 4u0a 4u0b 4u0c 4u0d 4u0e 4u0f 4xfx 4xfy 4xfz 4xro 4xrq 5hgm 5hgn 5hgo 5hgp 5irt 5jpa 5l93 5o2u 5upw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HGL)