Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  JOINT X-RAY/NEUTRON STRUCTURE OF HIV-1 PROTEASE TRIPLE MUTANT (V32I, I47V,V82I) WITH DARUNAVIR AT PH 4.3
 
Authors :  A. Y. Kovalevsky, A. Das
Date :  08 Oct 15  (Deposition) - 04 May 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION; NEUTRON DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protease Drug Resistant Mutant Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Gerlits, T. Wymore, A. Das, C. H. Shen, J. M. Parks, J. C. Smith, K. L. Weiss, D. A. Keen, M. P. Blakeley, J. M. Louis, P. Langan, I. T. Weber, A. Kovalevsky
Long-Range Electrostatics-Induced Two-Proton Transfer Captured By Neutron Crystallography In An Enzyme Catalytic Site.
Angew. Chem. Int. Ed. Engl. V. 55 4924 2016
PubMed-ID: 26958828  |  Reference-DOI: 10.1002/ANIE.201509989

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2, 2.7.7.-, 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B
    Organism Taxid: 11686
    Strain: ISOLATE BRU/LAI
    Synonym: PR160GAG-POL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 106)

Asymmetric/Biological Unit (2, 106)
No.NameCountTypeFull Name
10171Ligand/Ion(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
2DOD105Ligand/Ion

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ASP A:29 , ASP A:30 , ILE A:32 , VAL A:47 , GLY A:48 , ILE A:50 , ILE A:84 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , ILE B:32 , GLY B:48 , GLY B:49 , PRO B:81 , ILE B:82 , DOD B:307 , DOD B:315 , DOD B:326binding site for residue 017 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E5K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E5K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E5K)

(-) Exons   (0, 0)

(no "Exon" information available for 5E5K)

(-) 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
                  5e5k A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTIIEEMSLPGRWKPKMVGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPINIIGRNLLTQIGATLNF 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
                  5e5k B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTIIEEMSLPGRWKPKMVGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPINIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
   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 5E5K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E5K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E5K)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    017  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5e5k)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5e5k
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POL_HV1BR | P03367
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.7.49
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.7.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.1.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.1.13.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.1.26.13
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.4.23.16
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  POL_HV1BR | P03367
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1BR | P03367: 1a8g 1a8k 1a94 1aaq 1d4s 1d4y 1daz 1dif 1fqx 1hhp 1hni 1hpo 1hpx 1hsg 1hvl 1iiq 1izi 1lzq 1m0b 1mrw 1mrx 1msm 1msn 1nh0 1rl8 1sdt 1sdu 1sdv 1sgu 1sh9 1sp5 1u8g 1upj 1xl2 1xl5 1z8c 1zbg 1zj7 1zlf 1zpk 1zsf 1zsr 1ztz 2a1e 2az8 2az9 2azb 2azc 2b7z 2bb9 2fde 2fnd 2hb2 2hb4 2hc0 2hnd 2hny 2ien 2o4k 2o4l 2o4n 2o4p 2o4s 2p3b 2pk5 2pk6 2pqz 2pwc 2pwr 2pym 2pyn 2q63 2q64 2qak 2qci 2qd6 2qd7 2qd8 2qhc 2qnn 2qnp 2qnq 2r43 2upj 2z4o 2zga 2zye 3a2o 3bc4 3bgb 3bgc 3bhe 3bva 3bvb 3ckt 3djk 3dk1 3fx5 3ggu 3h5b 3i6o 3i8w 3jvw 3jvy 3jw2 3kdb 3kdc 3kdd 3ndu 3ndw 3ndx 3nls 3psu 3pwm 3pwr 3qbf 3qih 3qn8 3qp0 3qpj 3qrm 3qro 3qrs 3st5 3t11 3t3c 3tkg 3tkw 3tl9 3tof 3tog 3toh 3ttp 3u7s 3ucb 3uf3 3ufn 3uhl 3vf5 3vf7 3vfb 4dfg 4faf 4fe6 4fl8 4flg 4fm6 4gb2 4hdb 4hdf 4hdp 4he9 4heg 4hla 4j54 4j55 4j5j 4jec 4ll3 7upj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E5K)