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(-) Description

Title :  X-RAY STRUCTURE OF ESTER CHEMICAL ANALOGUE 'COVALENT DIMER' [ILE50,O-ILE50']HIV-1 PROTEASE COMPLEXED WITH MVT-101 INHIBITOR
 
Authors :  V. Y. Torbeev, S. B. H. Kent
Date :  13 Jul 10  (Deposition) - 02 Nov 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Barrel, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Y. Torbeev, H. Raghuraman, D. Hamelberg, M. Tonelli, W. M. Westler, E. Perozo, S. B. Kent
Protein Conformational Dynamics In The Mechanism Of Hiv-1 Protease Catalysis.
Proc. Natl. Acad. Sci. Usa V. 108 20982 2011
PubMed-ID: 22158985  |  Reference-DOI: 10.1073/PNAS.1111202108

(-) Compounds

Molecule 1 - PROTEASE COVALENT DIMER
    Chains: A
    EC Number: 3.4.23.16
    Engineered: YES
    Fragment: COVALENT DIMER HIV-1 PROTEASE
    Mutation: YES
    Other Details: CHEMICAL PROTEIN SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric/Biological Unit (6, 17)
No.NameCountTypeFull Name
12NC1Ligand/IonN-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
2ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
3NLE4Mod. Amino AcidNORLEUCINE
4OIL1Mod. Amino Acid(2S,3S)-2-HYDROXY-3-METHYLPENTANOIC ACID
5SO44Ligand/IonSULFATE ION
6YCM3Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:48 , VAL A:82 , ARG A:112 , ASP A:129 , GLY A:131 , ALA A:132 , ASP A:133 , ASP A:134 , GLY A:152 , GLY A:153 , OIL A:154 , VAL A:186 , HOH A:301 , HOH A:304 , HOH A:322 , HOH A:379 , HOH A:399BINDING SITE FOR RESIDUE 2NC A 204
2AC2SOFTWAREGLY A:177 , THR A:178 , ASN A:192 , GLN A:196 , HOH A:401 , SO4 A:504BINDING SITE FOR RESIDUE SO4 A 501
3AC3SOFTWAREARG A:14 , ARG A:118 , GLY A:120 , GLY A:121 , HOH A:329 , HOH A:357 , HOH A:391BINDING SITE FOR RESIDUE SO4 A 502
4AC4SOFTWARELYS A:149 , NLE A:150 , HOH A:310 , HOH A:386BINDING SITE FOR RESIDUE SO4 A 503
5AC5SOFTWARETRP A:6 , ARG A:191 , THR A:195 , HOH A:371 , SO4 A:501BINDING SITE FOR RESIDUE SO4 A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NXE)

(-) 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 O38716_9HIV1 | O38716 from UniProtKB/TrEMBL  Length:99

    Alignment length:203
                                                                                                                             99                                                                                                        
                                    10        20        30        40        50        60        70        80        90        |-         -         -         -         -         -         -         -         -         -         -   
         O38716_9HIV1     1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF--------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee.hhhh..ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nxe A   1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEElNLPGcWKPKlIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNFcGGGGPQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEElNLPGcWKPKlIGGxGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 203
                                    10        20        30     |  40|    |  50        60      | 70        80        90    |  100       110       120       130       140    |  150   |   160       170|      180       190       200   
                                                              36-NLE|    |                   67-ABA                      95-ABA|                                     140-NLE|    |   |              171-ABA                     199-ABA
                                                                   41-YCM|                                                   100-YCM                                      145-YCM|   |                                                 
                                                                        46-NLE                                                                                                 150-NLE                                                 
                                                                                                                                                                                   154-OIL
   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 3NXE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NXE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O38716_9HIV1 | O38716)
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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  3nxe
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  O38716_9HIV1 | O38716
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  3.4.23.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        O38716_9HIV1 | O38716: 2fgu 2fgv 2fns 2fnt 2je4 3i7e
UniProtKB/TrEMBL
        O38716_9HIV1 | O38716: 2o40

(-) Related Entries Specified in the PDB File

3fsm 3hau 3hdk 3hlo 3nwq 3nwx 3nxn 3nyg