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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH CARB-AD37
 
Authors :  C. A. Schiffer, M. N. L. Nalam
Date :  07 May 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Drug Design, Hiv-1 Protease, Protease Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chellappan, G. S. Kiran Kumar Reddy, A. Ali, M. N. Nalam, S. G. Anjum, H. Cao, V. Kairys, M. X. Fernandes, M. D. Altman, B. Tidor, T. M. Rana, C. A. Schiffer, M. K. Gilson
Design Of Mutation-Resistant Hiv Protease Inhibitors With The Substrate Envelope Hypothesis.
Chem. Biol. Drug Des. V. 69 298 2007
PubMed-ID: 17539822  |  Reference-DOI: 10.1111/J.1747-0285.2007.00514.X

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC35
    Expression System Strain: TAP56
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POL
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: SF2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MUU1Ligand/IonN-[(1S,2R)-1-BENZYL-3-{(CYCLOPROPYLMETHYL)[(3-METHOXYPHENYL)SULFONYL]AMINO}-2-HYDROXYPROPYL]-N'-METHYLSUCCINAMIDE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:68 , HIS A:69 , LYS A:70 , HOH A:565 , PRO B:1 , HOH B:561BINDING SITE FOR RESIDUE PO4 B 501
2AC2SOFTWAREARG A:14 , GLY A:16 , GLY A:17 , ARG B:14 , GLY B:16 , HOH B:517 , HOH B:556 , HOH B:559BINDING SITE FOR RESIDUE PO4 B 502
3AC3SOFTWAREMET A:36 , ASN A:37 , HOH A:573 , HOH A:585 , PRO B:39 , GLY B:40 , HOH B:555BINDING SITE FOR RESIDUE PO4 A 503
4AC4SOFTWARELYS A:20 , GLU A:21 , ASN A:83 , HOH A:531 , HOH A:549 , HOH A:570BINDING SITE FOR RESIDUE PO4 A 504
5AC5SOFTWAREPRO A:1 , HIS A:69 , HOH A:575 , PHE B:99BINDING SITE FOR RESIDUE ACT A 505
6AC6SOFTWARELYS A:7 , ARG A:8 , HOH A:551BINDING SITE FOR RESIDUE ACT A 506
7AC7SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , GLY A:48 , GLY A:49 , ILE A:50 , HOH A:511 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , GLY B:48 , GLY B:49 , VAL B:82 , ILE B:84BINDING SITE FOR RESIDUE MUU A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PSU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PSU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PSU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PSU)

(-) Exons   (0, 0)

(no "Exon" information available for 2PSU)

(-) 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:99
 aligned with O38723_9HIV1 | O38723 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38723_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d2psua_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2psuA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2psu A  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain A from PDB  Type:PROTEIN  Length:99
 aligned with O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d2psua_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2psuA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2psu A  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with O38723_9HIV1 | O38723 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38723_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d2psub_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2psuB00 B:1-99 Acid Proteases                                                                       CATH domains
           Pfam domains (1) ---RVP-2psuB01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-2psuB02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2psu B  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d2psub_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2psuB00 B:1-99 Acid Proteases                                                                       CATH domains
           Pfam domains (1) ---RVP-2psuB01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-2psuB02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2psu B  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_AA (368)

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O38732_9HIV1 | O38732)
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.

Chain A,B   (O38723_9HIV1 | O38723)
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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  2psu
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  O38732_9HIV1 | O38732
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 Related Entries

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

UniProtKB/Swiss-Prot
        O38732_9HIV1 | O38732: 2i0a 2i0d 2nxd 2nxl 2nxm 2psv 2q3k 2q54 2q55 2q5k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3gi4 3gi5 3gi6
UniProtKB/TrEMBL
        O38723_9HIV1 | O38723: 2i0a
        O38732_9HIV1 | O38732: 3dck 3dcr 3hzc 3i2l 3ia9 3sa3 3sa4 3sa5 3sa6 3sa7 3sa8 3sa9 3saa 3sab 3sac

(-) Related Entries Specified in the PDB File

2psv