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(-) Description

Title :  X-RAY STRUCTURE OF HIV-1 PROTEASE AND HYDRATED FORM OF KETOMETHYLENE ISOSTERE INHIBITOR
 
Authors :  V. Y. Torbeev, K. Mandal, V. A. Terechko, S. B. H. Kent
Date :  04 Jun 08  (Deposition) - 19 Aug 08  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1 Protease, Homodimer, Beta-Turn, Beta-Strand, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Y. Torbeev, K. Mandal, V. A. Terechko, S. B. H. Kent
Crystal Structure Of Chemically Synthesized Hiv-1 Protease And A Ketomethylene Isostere Inhibitor Based On The P2/Nc Cleavage Site
Bioorg. Med. Chem. Lett. V. 18 4554 2008
PubMed-ID: 18657969  |  Reference-DOI: 10.1016/J.BMCL.2008.07.039

(-) Compounds

Molecule 1 - CHEMICAL ANALOGUE HIV-1 PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Fragment: HIV-1 PROTEASE
    Other Details: TOTAL CHEMICAL PROTEIN SYNTHESIS UTILIZING SOLID PHASE PEPTIDE SYNTHESIS AND NATIVE CHEMICAL LIGATION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2KVS1Ligand/IonN~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-ACETYL-L-THREONYL)AMINO]-3-METHYLPENT-4-ENOYL}AMINO)-2-BUTYL-4,4-DIHYDROXYNONANOYL]-L-GLUTAMINYL-L-ARGININAMIDE
3NLE4Mod. Amino AcidNORLEUCINE
4YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , GLY A:48 , GLY A:49 , HOH A:136 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , ILE B:47 , GLY B:48 , GLY B:49 , ILE B:50 , VAL B:82 , HOH B:257 , HOH B:258 , HOH B:259 , HOH B:260BINDING SITE FOR RESIDUE KVS B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DCR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DCR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DCR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DCR)

(-) Exons   (0, 0)

(no "Exon" information available for 3DCR)

(-) 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 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 --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dcrA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3dcr A  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEElNLPGcWKPKlIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30     |  40|    |  50        60      | 70        80        90    |    
                                                              36-NLE|    |                   67-ABA                      95-ABA
                                                                   41-YCM|                                                     
                                                                        46-NLE                                                 


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 --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dcrB00 B: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
                  3dcr B  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEElNLPGcWKPKlIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30     |  40|    |  50        60      | 70        80        90    |    
                                                              36-NLE|    |                   67-ABA                      95-ABA
                                                                   41-YCM|                                                     
                                                                        46-NLE
   Legend:   → Mismatch (orange background)
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  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 3DCR)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DCR)

(-) Gene Ontology  (4, 4)

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.

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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 2psu 2psv 2q3k 2q54 2q55 2q5k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3gi4 3gi5 3gi6
UniProtKB/TrEMBL
        O38732_9HIV1 | O38732: 3dck 3hzc 3i2l 3ia9 3sa3 3sa4 3sa5 3sa6 3sa7 3sa8 3sa9 3saa 3sab 3sac

(-) Related Entries Specified in the PDB File

3dck