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(-) Description

Title :  APO HIV PROTEASE (PR) DIMER IN CLOSED FORM WITH 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 :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apo Protease, Allostery, Fragment Binding, Closed Form, Hydrolase (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
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: R8
    Synonym: PR, RETROPEPSIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
11F11Ligand/Ion1H-INDOLE-6-CARBOXYLIC ACID
2DMS5Ligand/IonDIMETHYL SULFOXIDE
3EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:70 , LYS B:43 , LYS B:45 , GLN B:58BINDING SITE FOR RESIDUE DMS A 101
02AC2SOFTWAREGLY A:27 , ALA A:28 , ASP A:29 , HOH A:247BINDING SITE FOR RESIDUE DMS A 102
03AC3SOFTWARELEU A:19 , ARG A:87 , THR A:91 , EDO A:105 , HOH A:218 , LEU B:5 , TRP B:6BINDING SITE FOR RESIDUE DMS A 103
04AC4SOFTWAREGLU A:34 , GLU A:35 , GLY A:78 , PRO A:79 , THR A:80 , TRP B:42BINDING SITE FOR RESIDUE EDO A 104
05AC5SOFTWARELEU A:19 , ASN A:88 , GLN A:92 , DMS A:103 , HOH A:248BINDING SITE FOR RESIDUE EDO A 105
06AC6SOFTWARETRP A:42 , PRO 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:205 , HOH A:221 , TRP B:6BINDING SITE FOR RESIDUE 1F1 A 106
07AC7SOFTWAREGLY B:27 , ALA B:28 , ASP B:29BINDING SITE FOR RESIDUE DMS B 101
08AC8SOFTWAREGLU A:65 , GLY A:68 , HOH A:223 , ARG B:41 , TRP B:42 , LYS B:43 , GLN B:58 , ASP B:60BINDING SITE FOR RESIDUE DMS B 102
09AC9SOFTWAREASP B:30 , GLN B:58 , HOH B:250BINDING SITE FOR RESIDUE EDO B 103
10BC1SOFTWARELEU A:19 , PRO B:39 , GLY B:40 , ARG B:41 , HOH B:206BINDING SITE FOR RESIDUE EDO B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 4EJ8)

(-) 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 d4ej8a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4ej8 A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMNLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d4ej8b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......eee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4ej8 B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMNLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EJ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EJ8)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4ej8
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  POL_HV1Z2 | P12499
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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 4ejd 4ejk 4ejl 4k4p 4k4q 4k4r

(-) Related Entries Specified in the PDB File

4ejd 4ejk 4ejl