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(-) Description

Title :  CRYSTAL STRUCTURE OF A TETHERED DIMER OF HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR
 
Authors :  T. N. Bhat, E. T. Baldwin, J. W. Erickson
Date :  22 Jun 94  (Deposition) - 15 Oct 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(Acid Protease) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Bhat, E. T. Baldwin, B. Liu, Y. S. Cheng, J. W. Erickson
Crystal Structure Of A Tethered Dimer Of Hiv-1 Proteinase Complexed With An Inhibitor.
Nat. Struct. Biol. V. 1 552 1994
PubMed-ID: 7664084  |  Reference-DOI: 10.1038/NSB0894-552
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SYNTHETIC GENE
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1A791Ligand/IonN-{1-BENZYL-(2S,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8A , ARG A:8B , ASP A:25A , ASP A:25B , GLY A:27A , GLY A:27B , ALA A:28A , ALA A:28B , ASP A:29A , ASP A:29B , GLY A:48A , GLY A:48B , GLY A:49A , ILE A:50B , VAL A:82A , VAL A:82B , ILE A:84A , ILE A:84B , HOH A:415BINDING SITE FOR RESIDUE A79 A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HVC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:203 -Gly A:204
2Gly A:16A-Gly A:17A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HVC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HVC)

(-) Exons   (0, 0)

(no "Exon" information available for 1HVC)

(-) 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:203
 aligned with O92139_9HIV1 | O92139 from UniProtKB/TrEMBL  Length:99

    Alignment length:203
                                                                                                                                    1                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96   
         O92139_9HIV1     - --------------------------------------------------------------------------------------------------------PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
               SCOP domains d1hvca1 A:1B-99B Human immunodeficiency virus type 1 protease                                      -----d1hvca2 A:1A-99A Human immunodeficiency virus type 1 protease                                       SCOP domains
               CATH domains 1hvcA01 A:1B-99B Acid Proteases                                                                    -----1hvcA02 A:1A-99A Acid Proteases                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeee....eeeeee......eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee.......ee......eeeeee..eeeeeee.......eee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hvc A  1B PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFGGSSGPQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99A
                            |||||||10B|||||||20B|||||||30B|||||||40B|||||||50B|||||||60B|||||||70B|||||||80B|||||||90B|||||||200   |||||6A|||||||16A|||||||26A|||||||36A|||||||46A|||||||56A|||||||66A|||||||76A|||||||86A|||||||96A|||
                            |||||||9B||||||18B||||||27B||||||36B||||||45B||||||54B||||||63B||||||72B||||||81B||||||90B||||||99B| 204|||||||9A||||||18A||||||27A||||||36A||||||45A||||||54A||||||63A||||||72A||||||81A||||||90A||||||99A
                           1B||||||10B||||||19B||||||28B||||||37B||||||46B||||||55B||||||64B||||||73B||||||82B||||||91B||||||200   1A||||||10A||||||19A||||||28A||||||37A||||||46A||||||55A||||||64A||||||73A||||||82A||||||91A||||||| 
                            2B||||||11B||||||20B||||||29B||||||38B||||||47B||||||56B||||||65B||||||74B||||||83B||||||92B||||||      2A||||||11A||||||20A||||||29A||||||38A||||||47A||||||56A||||||65A||||||74A||||||83A||||||92A|||||| 
                             3B||||| 12B||||| 21B||||| 30B||||| 39B||||| 48B||||| 57B||||| 66B||||| 75B||||| 84B||||| 93B|||||       3A||||| 12A||||| 21A||||| 30A||||| 39A||||| 48A||||| 57A||||| 66A||||| 75A||||| 84A||||| 93A||||| 
                              4B||||  13B||||  22B||||  31B||||  40B||||  49B||||  58B||||  67B||||  76B||||  85B||||  94B||||        4A||||  13A||||  22A||||  31A||||  40A||||  49A||||  58A||||  67A||||  76A||||  85A||||  94A|||| 
                               5B|||   14B|||   23B|||   32B|||   41B|||   50B|||   59B|||   68B|||   77B|||   86B|||   95B|||         5A|||   14A|||   23A|||   32A|||   41A|||   50A|||   59A|||   68A|||   77A|||   86A|||   95A||| 
                                6B||    15B||    24B||    33B||    42B||    51B||    60B||    69B||    78B||    87B||    96B||          6A||    15A||    24A||    33A||    42A||    51A||    60A||    69A||    78A||    87A||    96A|| 
                                 7B|     16B|     25B|     34B|     43B|     52B|     61B|     70B|     79B|     88B|     97B|           7A|     16A|     25A|     34A|     43A|     52A|     61A|     70A|     79A|     88A|     97A| 
                                  8B      17B      26B      35B      44B      53B      62B      71B      80B      89B      98B            8A      17A      26A      35A      44A      53A      62A      71A      80A      89A      98A 


Chain A from PDB  Type:PROTEIN  Length:203
 aligned with Q4VE97_9HIV1 | Q4VE97 from UniProtKB/TrEMBL  Length:328

    Alignment length:326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
         Q4VE97_9HIV1     1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQILVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPIFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGFTTPDKKHQKEPPF 326
               SCOP domains d1hvca1 A:1B-99B Human immunodeficiency virus type 1 protease                                      ------------------d1hvca      2 A:1A-           99A                                          Human immunodeficien                                   cy vir  us typ    e 1 protease                                                  SCOP domains
               CATH domains 1hvcA01 A:1B-99B Acid Proteases                                                                    ------------------1hvcA0      2 A:1A-           99A                                          Acid Proteases                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeee....eeeeee......eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee.-------------......ee...------...eeee-----------ee.-----------------------------------------.eeeeeee.......eee...-----------------------------------.....e--eeeeee----..eeeeeeeeeeeeeee..eeeee-eeeee.....eeh-hhhhh....eee---------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hvc A  1B PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF-------------GGSSGPQITLW------QRPLVTI-----------KIG-----------------------------------------GQLKEALLDTGADDTVLEEMS-----------------------------------LPGRWK--PKMIGG----IGGFIKVRQYDQILIEICGHKAIG-TVLVGPTPVNIIG-RNLLTQIGCTLN---------F 99A
                            |||||||10B|||||||20B|||||||30B|||||||40B|||||||50B|||||||60B|||||||70B|||||||80B|||||||90B|||||||||-         -  |   ||3A|||     7A||||||   -       16A         -         -         -         - ||||||25A|||||||35A||       -         -         -       40A|||  ||48A|    ||54A|||||||64A|||||||||-|||||||83A||| |||92A||||||   -     |
                            |||||||9B||||||18B||||||27B||||||36B||||||45B||||||54B||||||63B||||||72B||||||81B||||||90B||||||99B           200 204||||||     7A||||||         14A||                                       17A||||||26A||||||35A||                                 38A|||||  |47A||  50A||||||59A||||||68A||||| |77A||||||86A ||||||95A|||       99A
                           1B||||||10B||||||19B||||||28B||||||37B||||||46B||||||55B||||||64B||||||73B||||||82B||||||91B|||||||                  1A|||||      8A|||||          15A|                                        18A||||||27A||||||36A|                                  39A||||  ||48A|   51A||||||60A||||||69A|||| ||78A|||||||87A||||||96A||          
                            2B||||||11B||||||20B||||||29B||||||38B||||||47B||||||56B||||||65B||||||74B||||||83B||||||92B||||||                   2A||||       9A||||           16A                                         19A||||||28A||||||37A                                   40A|||  |||49A    52A||||||61A||||||70A||| |||79A|||||| 88A||||||97A|          
                             3B||||| 12B||||| 21B||||| 30B||||| 39B||||| 48B||||| 57B||||| 66B||||| 75B||||| 84B||||| 93B|||||                    3A|||       10A|||                                                        20A||||| 29A|||||                                       41A||  |||        53A||||| 62A||||| 71A|| ||| 80A|||||  89A||||| 98A          
                              4B||||  13B||||  22B||||  31B||||  40B||||  49B||||  58B||||  67B||||  76B||||  85B||||  94B||||                     4A||        11A||                                                         21A||||  30A||||                                        42A|  |||         54A||||  63A||||  72A| |||  81A||||   90A||||              
                               5B|||   14B|||   23B|||   32B|||   41B|||   50B|||   59B|||   68B|||   77B|||   86B|||   95B|||                      5A|         12A|                                                          22A|||   31A|||                                         43A  |||          55A|||   64A|||   73A |||   82A|||    91A|||              
                                6B||    15B||    24B||    33B||    42B||    51B||    60B||    69B||    78B||    87B||    96B||                       6A          13A                                                           23A||    32A||                                            44A||           56A||    65A||     74A||    83A||     92A||              
                                 7B|     16B|     25B|     34B|     43B|     52B|     61B|     70B|     79B|     88B|     97B|                                                                                                  24A|     33A|                                             45A|            57A|     66A|      75A|     84A|      93A|              
                                  8B      17B      26B      35B      44B      53B      62B      71B      80B      89B      98B                                                                                                   25A      34A                                              46A             58A      67A       76A      85A       94A
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HVC)

(-) Gene Ontology  (8, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4VE97_9HIV1 | Q4VE97)
molecular function
    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: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: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: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.
biological process
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A   (O92139_9HIV1 | O92139)
molecular function
    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: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: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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  1hvc
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 Related Entries

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

UniProtKB/Swiss-Prot
        O92139_9HIV1 | O92139: 2bb9
UniProtKB/TrEMBL
        O92139_9HIV1 | O92139: 1hvi 1zp8 2bqv 2i4w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HVC)