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(-) Description

Title :  CRYSTAL STRUCTURE OF KB-19 COMPLEXED WITH WILD TYPE HIV-1 PROTEASE
 
Authors :  M. N. L. Nalam, C. A. Schiffer, A. Ali, K. K. Reddy, H. Cao, S. G. Anjum, T. M
Date :  10 Aug 06  (Deposition) - 19 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Drug Design, Hiv-1 Protease, Protease Inhibitors, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ali, G. S. Reddy, H. Cao, S. G. Anjum, M. N. Nalam, C. A. Schiffer, T. M. Rana
Discovery Of Hiv-1 Protease Inhibitors With Picomolar Affinities Incorporating N-Aryl-Oxazolidinone-5-Carboxamide As Novel P2 Ligands.
J. Med. Chem. V. 49 7342 2006
PubMed-ID: 17149864  |  Reference-DOI: 10.1021/JM060666P

(-) 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, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MUI1Ligand/Ion(5S)-3-(4-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , GLY A:16 , GLY A:17 , HOH A:622 , HOH A:665 , GLY B:16 , HOH B:525 , HOH B:559BINDING SITE FOR RESIDUE PO4 B 501
2AC2SOFTWAREGLY A:68 , HIS A:69 , LYS A:70 , HOH A:625 , PRO B:1 , HOH B:577BINDING SITE FOR RESIDUE PO4 B 503
3AC3SOFTWAREMET A:36 , ASN A:37 , HOH A:670 , PRO B:39 , GLY B:40 , HOH B:514BINDING SITE FOR RESIDUE PO4 A 504
4AC4SOFTWARELYS A:20 , GLU A:21 , ASN A:83 , HOH A:637 , HOH A:659 , HOH A:664BINDING SITE FOR RESIDUE PO4 A 505
5AC5SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , GLY A:48 , ILE A:50 , VAL A:82 , GOL A:601 , HOH A:604 , HOH A:641 , ARG B:8 , 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 MUI A 200
6AC6SOFTWAREGLY A:49 , PHE A:53 , MUI A:200 , HOH A:644 , HOH A:661 , THR B:91 , GLN B:92 , HOH B:554BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I0A)

(-) Exons   (0, 0)

(no "Exon" information available for 2I0A)

(-) 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 d2i0aa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2i0aA00 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
                  2i0a 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 d2i0aa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2i0aA00 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
                  2i0a 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 d2i0ab_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2i0aB00 B:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2i0a 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 d2i0ab_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2i0aB00 B:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2i0a 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  (0, 0)

(no "Pfam Domain" information available for 2I0A)

(-) 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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  O38732_9HIV1 | O38732
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 Related Entries

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

UniProtKB/Swiss-Prot
        O38732_9HIV1 | O38732: 2i0d 2nxd 2nxl 2nxm 2psu 2psv 2q3k 2q54 2q55 2q5k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3gi4 3gi5 3gi6
UniProtKB/TrEMBL
        O38723_9HIV1 | O38723: 2psu
        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

1f7a CRYSTAL STRUCTURE OF THE CAPSID-P2 SUBSTRATE PEPTIDE COMPLEXED WITH WILD TYPE D25N HIV-1 PROTEASE USED AS THE STARTING MODEL
2i0d CRYSTAL STRUCTURE OF 3-ACETYL DERIVATIVE OF KB-19 COMPLEXED WITH THE WILD TYPE HIV-1 PROTEASE