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 :  X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A COMPLEX BETWEEN A SYNTHETIC PROTEASE OF HUMAN IMMUNODEFICIENCY VIRUS 1 AND A SUBSTRATE-BASED HYDROXYETHYLAMINE INHIBITOR
 
Authors :  A. L. Swain, M. M. Miller, J. Green, D. H. Rich, J. Schneider, S. B. H. Kent A. Wlodawer
Date :  13 Sep 90  (Deposition) - 15 Jul 93  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Acid Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Swain, M. M. Miller, J. Green, D. H. Rich, J. Schneider, S. B. Kent, A. Wlodawer
X-Ray Crystallographic Structure Of A Complex Between A Synthetic Protease Of Human Immunodeficiency Virus 1 And A Substrate-Based Hydroxyethylamine Inhibitor.
Proc. Natl. Acad. Sci. Usa V. 87 8805 1990
PubMed-ID: 2247451  |  Reference-DOI: 10.1073/PNAS.87.22.8805
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - INHIBITOR ACE-SER-LEU-ASN-PHE-PSI(CH(OH)-CH2N)-PRO-ILE VME (JG-365)
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2ACE1Mod. Amino AcidACETYL GROUP
3JG31Mod. Amino Acid1-[(2S,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-L-PROLINE
4VME1Mod. Amino AcidMETHYL L-VALINATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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 , GLY A:49 , ILE A:50 , HOH A:318 , HOH A:378 , ARG B:8 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , ILE B:47 , GLY B:48 , GLY B:49 , ILE B:50 , VAL B:82 , ILE B:84 , HOH C:301 , HOH C:395BINDING SITE FOR CHAIN C OF INHIBITOR ACE-SER- LEU-ASN-PHE-PSI(CH(OH)-CH2N)-PRO-ILE VME
2DTAUNKNOWNASP A:25 , THR A:26 , GLY A:27BINDING SITE
3DTBUNKNOWNASP B:25 , THR B:26 , GLY B:27BINDING SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 7HVP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 7HVP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 7HVP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 7HVP)

(-) Exons   (0, 0)

(no "Exon" information available for 7HVP)

(-) 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 d7hvpa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 7hvpA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeee....eeeeeee..eeeeeeee.....eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee....eeehhhhhhhhh.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  7hvp A  1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30        40        50        60      | 70        80        90    |    
                                                                                             67-ABA                      95-ABA


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d7hvpb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 7hvpB00 B:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeee....eeeeeee..eeeeeeee.....eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee....eeehhhhhhhhh.eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  7hvp B  1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEIaGHKAIGTVLVGPTPVNIIGRNLLTQIGaTLNF 99
                                    10        20        30        40        50        60      | 70        80        90    |    
                                                                                             67-ABA                      95-ABA


Chain C from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  7hvp C  0 xSLNxIx  6
                            |   | |
                            |   | |
                            0-ACE |
                                4-JG3
                                  6-VME
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 7HVP)

(-) 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
    ABA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JG3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    VME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    DTA  [ RasMol ]  +environment [ RasMol ]
    DTB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 7hvp)
 

(-) 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
  7hvp
    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_HV1A2 | P03369
    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)
  (no 'Enzyme Classificator' available)
    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_HV1A2 | P03369
    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_HV1A2 | P03369: 1aid 1b6j 1b6k 1b6l 1b6m 1b6p 1cpi 1d4k 1d4l 1f7a 1kj4 1kj7 1kjf 1kjg 1kjh 1kzk 1mt7 1mt8 1mt9 1mtb 1mtr 1n49 1t3r 1tsq 1tsu 1ytg 1yth 1z1h 1z1r 2aid 2f3k 2fgu 2fgv 2fns 2fnt 2j9j 2j9k 2je4 2nxd 2nxl 2nxm 2q3k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3aid 3bxr 3bxs 3ekp 3ekq 3ekt 3ekv 3ekw 3ekx 3eky 3el0 3el1 3el4 3el5 3el9 3em3 3em4 3em6 3fsm 3gi0 3gi4 3gi5 3gi6 3hau 3haw 3hbo 3hdk 3hlo 3hvp 3hzc 3i2l 3i7e 3iaw 3ka2 3lzv 3mxd 3mxe 3nwq 3nwx 3nxn 3nyg 3o9f 3o9g 3o9h 3o9i 3oxv 3oxw 3oxx 3oy4 3r4b 4ep2 4ep3 4epj 4eq0 4eqj 4f73 4f74 4f75 4f76 4hvp 4obd 4obf 4obg 4obh 4obj 4obk 4qj2 4qj6 4qj7 4qj8 4qj9 4qja 8hvp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 7HVP)