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(-) Description

Title :  CRYSTAL STRUCTURE OF NELFINAVIR-RESISTANT, INACTIVE HIV-1 PROTEASE (D30N/N88D) IN COMPLEX WITH THE P1-P6 SUBSTRATE.
 
Authors :  M. Kolli
Date :  07 Jan 14  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Co-Evolution, Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kolli, A. Ozen, N. Kurt-Yilmaz, C. A. Schiffer
Hiv-1 Protease-Substrate Coevolution In Nelfinavir Resistance.
J. Virol. V. 88 7145 2014
PubMed-ID: 24719428  |  Reference-DOI: 10.1128/JVI.00266-14

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B, C, D
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC35
    Expression System Strain: TAP106
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11685
    Strain: GROUP M SUBTYPE B (ISOLATE ARV2/SF2)
    Synonym: PR, RETROPEPSIN
 
Molecule 2 - P1-P6 PEPTIDE
    Chains: E, F
    Engineered: YES
    Fragment: UNP RESIDUES 446-455
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2GOL4Ligand/IonGLYCEROL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:8 , ARG B:87 , ARG E:9BINDING SITE FOR RESIDUE GOL A 101
02AC2SOFTWAREGLU A:35 , MET A:36 , ASN A:37 , HOH A:238 , PRO B:39 , GLY B:40BINDING SITE FOR RESIDUE PO4 A 102
03AC3SOFTWAREARG A:14 , ILE A:15 , GLY A:16 , GLY A:17 , PRO A:63 , ILE A:64 , HOH A:201BINDING SITE FOR RESIDUE EDO A 103
04AC4SOFTWAREARG A:14 , CYS A:67 , GLY A:68 , HOH A:254BINDING SITE FOR RESIDUE EDO A 104
05AC5SOFTWAREARG A:87 , LYS B:7 , ARG B:8 , HOH B:212BINDING SITE FOR RESIDUE GOL B 101
06AC6SOFTWAREGLY A:40 , GLN B:18 , LYS B:20 , ASN B:37BINDING SITE FOR RESIDUE EDO B 102
07AC7SOFTWAREARG C:14 , GLY C:16 , GLY C:17 , GLY D:16 , GLY D:17 , PRO D:63 , HOH D:208BINDING SITE FOR RESIDUE GOL C 101
08AC8SOFTWARELYS C:7 , ARG C:8 , ARG F:9BINDING SITE FOR RESIDUE GOL C 102
09AC9SOFTWARETRP B:42 , LYS B:55 , ARG B:57 , VAL C:11 , THR C:12 , CYS C:67 , HOH C:225BINDING SITE FOR RESIDUE PO4 C 103
10BC1SOFTWARELYS C:70BINDING SITE FOR RESIDUE EDO C 105
11BC2SOFTWARELYS D:20 , GLU D:21 , ASN D:83BINDING SITE FOR RESIDUE EDO D 101
12BC3SOFTWARETRP D:6 , LYS D:7 , ARG D:8 , HOH D:207BINDING SITE FOR RESIDUE EDO D 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OBG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OBG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OBG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OBG)

(-) Exons   (0, 0)

(no "Exon" information available for 4OBG)

(-) Sequences/Alignments

Asymmetric 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:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4obg A  1 PQITLWKRPLVTIRIGGQLKEALLNTGADNTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRDLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4obg B  1 PQITLWKRPLVTIRIGGQLKEALLNTGADNTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRDLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee.........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4obg C  1 PQITLWKRPLVTIRIGGQLKEALLNTGADNTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRDLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain D from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4obg D  1 PQITLWKRPLVTIRIGGQLKEALLNTGADNTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRDLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain E from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ......ee.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  4obg E  1 RPGNFLQSRP 10
                                    10


Chain F from PDB  Type:PROTEIN  Length:9
                                        
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                  4obg F  1 RPGNFLQSR  9
   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 4OBG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OBG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OBG)

(-) Gene Ontology  (47, 65)

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  POL_HV1A2 | P03369
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV1A2 | P03349: 4obd 4obf 4obh 4obj 4obk 4qj2 4qj6 4qj7 4qj8 4qj9 4qja
        POL_HV1A2 | P03369: 1aid 1b6j 1b6k 1b6l 1b6m 1b6p 1cpi 1d4k 1d4l 1f7a 1kj4 1kj7 1kjf 1kjg 1kjh 1kzk 1mt7 1mt8 1mt9 1mtb 1mtr 1n49 1t3r 1tsq 1tsu 1ytg 1yth 1z1h 1z1r 2aid 2f3k 2fgu 2fgv 2fns 2fnt 2j9j 2j9k 2je4 2nxd 2nxl 2nxm 2q3k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3aid 3bxr 3bxs 3ekp 3ekq 3ekt 3ekv 3ekw 3ekx 3eky 3el0 3el1 3el4 3el5 3el9 3em3 3em4 3em6 3fsm 3gi0 3gi4 3gi5 3gi6 3hau 3haw 3hbo 3hdk 3hlo 3hvp 3hzc 3i2l 3i7e 3iaw 3ka2 3lzv 3mxd 3mxe 3nwq 3nwx 3nxn 3nyg 3o9f 3o9g 3o9h 3o9i 3oxv 3oxw 3oxx 3oy4 3r4b 4ep2 4ep3 4epj 4eq0 4eqj 4f73 4f74 4f75 4f76 4hvp 4obd 4obf 4obh 4obj 4obk 4qj2 4qj6 4qj7 4qj8 4qj9 4qja 7hvp 8hvp

(-) Related Entries Specified in the PDB File

4obd 4obf 4obh 4obj 4obk