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(-) Description

Title :  HIV PROTEASE (PR) DIMER IN CLOSED FORM WITH PEPSTATIN IN ACTIVE SITE AND FRAGMENT 1F1 IN THE OUTSIDE/TOP OF FLAP
 
Authors :  T. Tiefenbrunn, C. D. Stout
Date :  06 Apr 12  (Deposition) - 01 May 13  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Apo Protease, Allostery, Fragment Binding, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tiefenbrunn, S. Forli, M. M. Baksh, M. W. Chang, M. Happer, Y. C. Lin, A. L. Perryman, J. K. Rhee, B. E. Torbett, A. J. Olson, J. H. Elder, M. G. Finn, C. D. Stout
Small Molecule Regulation Of Protein Conformation By Bindin In The Flap Of Hiv Protease.
Acs Chem. Biol. V. 8 1223 2013
PubMed-ID: 23540839  |  Reference-DOI: 10.1021/CB300611P

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 490-588
    Gene: POL
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: R8
    Synonym: PR, RETROPEPSIN
 
Molecule 2 - PEPSTATIN
    Chains: C
    Engineered: YES
    Organism Scientific: STREPTOMYCES ARGENTEOLUS SUBSP. TOYONAKENSIS
    Organism Taxid: 285516
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
11F11Ligand/Ion1H-INDOLE-6-CARBOXYLIC ACID
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4IVA1Mod. Amino AcidISOVALERIC ACID
5STA2Mod. Amino AcidSTATINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:10 , VAL A:11 , THR A:12 , CYS A:67 , HOH A:207 , LYS B:7 , HOH B:246BINDING SITE FOR RESIDUE BME A 101
2AC2SOFTWAREPRO A:44 , LYS A:45 , LYS A:55 , VAL A:56 , ARG A:57 , THR A:91 , GLN A:92 , GLY A:94 , HOH A:209 , HOH A:278 , HOH B:233BINDING SITE FOR RESIDUE 1F1 A 102
3AC3SOFTWAREGLY A:49 , GLY A:51 , GLY A:52 , PRO B:44 , MET B:46 , LYS B:55 , PRO B:81 , HOH B:225 , HOH B:251 , HOH C:104BINDING SITE FOR RESIDUE GOL B 101
4AC4SOFTWARELYS A:7 , HOH A:227 , VAL B:11 , CYS B:67 , BME B:103BINDING SITE FOR RESIDUE BME B 102
5AC5SOFTWARELYS A:7 , HOH A:227 , THR B:12 , CYS B:67 , BME B:102BINDING SITE FOR RESIDUE BME B 103
6AC6SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , LYS A:45 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:84 , ARG B:8 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:48 , HOH B:231 , HOH C:102 , HOH C:103 , HOH C:105BINDING SITE FOR CHAIN C OF PEPSTATIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EJD)

(-) 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......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4ejd 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.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4ejd 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
                  4ejd C  1 xVVxAx  6
                            |  | |
                            1-IVA|
                               4-STA
                                 6-STA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4EJD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1Z2 | P12499: 1e28 1hxw 1p7q 1pro 1q94 1vij 1vik 2wkz 2wl0 2xye 2xyf 3kf0 3kfn 3kfp 3kfr 3kfs 3w39 4dqb 4dqc 4dqe 4dqf 4dqg 4dqh 4e43 4ej8 4ejk 4ejl 4k4p 4k4q 4k4r

(-) Related Entries Specified in the PDB File

4ej8 4ejk 4ejl