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(-) Description

Title :  HIV PROTEASE (PR) DIMER IN CLOSED FORM WITH PEPSTATIN IN ACTIVE SITE AND FRAGMENT AK-2097 IN THE OUTSIDE/TOP OF FLAP
 
Authors :  T. Tiefenbrunn, A. Kislukhin, M. G. Finn, C. D. Stout
Date :  26 Jun 14  (Deposition) - 24 Sep 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Apo Protease, Allostery, Fragment Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Deng, S. Forli, P. He, A. Perryman, L. Wickstrom, R. S. Vijayan, T. Tiefenbrunn, D. Stout, E. Gallicchio, A. J. Olson, R. M. Levy
Distinguishing Binders From False Positives By Free Energy Calculations: Fragment Screening Against The Flap Site Of Hiv Protease.
J. Phys. Chem. B V. 119 976 2015
PubMed-ID: 25189630  |  Reference-DOI: 10.1021/JP506376Z

(-) Compounds

Molecule 1 - HIV PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 21A+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: POL
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - PEPSTATIN
    Chains: C
    Engineered: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IVA1Mod. Amino AcidISOVALERIC ACID
3K971Ligand/Ion3-(MORPHOLIN-4-YLMETHYL)-1H-INDOLE-6-CARBOXYLIC ACID
4STA2Mod. Amino AcidSTATINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , LYS A:45 , MET A:46 , LYS A:55 , VAL A:56 , ARG A:57 , HIS A:69 , LYS A:70 , THR A:91 , GLN A:92 , ILE A:93 , GLY A:94 , HOH A:206 , HOH A:207 , TRP B:6binding site for residue K97 A 101
2AC2SOFTWAREGLY A:49 , GLY A:52 , PRO B:44 , HOH B:202 , HOH B:203binding site for residue GOL B 101
3AC3SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , ILE A:84 , ARG B:8 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , ILE B:47 , GLY B:48 , ILE B:50 , HOH B:224 , HOH C:101 , HOH C:102binding site for Pepstatin chain C

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TVG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TVG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TVG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TVG)

(-) Exons   (0, 0)

(no "Exon" information available for 4TVG)

(-) 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
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- 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
                  4tvg A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4tvg B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain C from PDB  Type:PROTEIN  Length:6
                                     
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .ee... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                  4tvg C  1 xVVxAx  6
                            |  | |
                            1-IVA|
                               4-STA
                                 6-STA
   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 4TVG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TVG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TVG)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q90EA1_9HIV1 | Q90EA1: 4tvh

(-) Related Entries Specified in the PDB File

4tvh