Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  PFV INTEGRASE TARGET CAPTURE COMPLEX, APO FORM (TCC-APO), AT 3.15 A RESOLUTION
 
Authors :  G. N. Maertens, P. Cherepanov
Date :  17 Mar 12  (Deposition) - 23 May 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B,C,D,T
Biol. Unit 1:  A,B,C,D,T  (2x)
Keywords :  Protein-Dna Complex, Tetramer, Hhcc Motif, Endonuclease, Metal- Binding, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Nucleus, Transferase, Virion, Dna-Binding, Zinc-Binding, Viral Protein, Recombination, Viral Protein-Dna Complex, Recombination-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hare, G. N. Maertens, P. Cherepanov
3'-Processing And Strand Transfer Catalysed By Retroviral Integrase In Crystallo.
Embo J. V. 468 326 2012
PubMed-ID: 22580823  |  Reference-DOI: 10.1038/EMBOJ.2012.118
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRO-POL POLYPROTEIN
    Chains: A, B
    EC Number: 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSSH6P-PFV-INFL
    Expression System Strain: PC2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 752-1143
    Gene: POL
    Organism Common: SFVCPZ(HU)
    Organism Scientific: HUMAN SPUMARETROVIRUS
    Organism Taxid: 11963
    Strain: HSRV2
    Synonym: PR125POL, PROTEASE/REVERSE TRANSCRIPTASE/RIBONUCLEASE H, P87PRO-RT-RNASEH, PROTEASE/REVERSE TRANSCRIPTASE, P65PRO-RT, RIBONUCLEASE H, RNASE H, INTEGRASE, IN, P42IN
 
Molecule 2 - DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')
    Chains: C
    Engineered: YES
    Other Details: VIRAL DNA
    Other Details - Source: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')
    Chains: D
    Engineered: YES
    Other Details: VIRAL DNA
    Other Details - Source: SYNTHETIC DNA
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*GP*CP*AP*CP*GP*TP* GP*CP*CP*TP*CP*GP*GP*G)-3')
    Chains: T
    Engineered: YES
    Other Details: TARGET DNA
    Other Details - Source: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDT
Biological Unit 1 (2x): ABCDT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:62 , HIS A:66 , CYS A:96 , CYS A:99BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARELYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260 , LEU B:261BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E7J)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:131 -Pro A:132
2Leu A:358 -Gly A:359
3Gly B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E7J)

(-) Exons   (0, 0)

(no "Exon" information available for 4E7J)

(-) Sequences/Alignments

Asymmetric 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.............ee..eeeeee..eeeee.hhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhh....................eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhhhh....................eeee...............eeeeeeee..eeeee.....eeeee...eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7j A  10 AELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSH 374
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369     


Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee............eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh........hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e7j B 116 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPF 278
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275   


Chain C from PDB  Type:DNA  Length:19
                                                   
                 4e7j C   1 ATTGTCATGGAATTTCGCA  19
                                    10         


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4e7j D   1 TGCGAAATTCCATGACA  17
                                    10       


Chain T from PDB  Type:DNA  Length:16
                                                
                 4e7j T  -6 CACGTGCTAGCACGTG   9
                                     3
   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 4E7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E7J)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:131 - Pro A:132   [ RasMol ]  
    Gly B:131 - Pro B:132   [ RasMol ]  
    Leu A:358 - Gly A:359   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4e7j
    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_FOAMV | P14350
    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)
  2.7.7.49
    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
  3.1.26.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.4.23.-
    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_FOAMV | P14350
    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_FOAMV | P14350: 2lsn 2x6n 2x6s 2x74 2x78 3dlr 3l2q 3l2r 3l2u 3l2v 3l2w 3os0 3os1 3os2 3oy9 3oya 3oyb 3oyc 3oyd 3oye 3oyf 3oyg 3oyh 3oyi 3oyj 3oyk 3oyl 3oym 3oyn 3s3m 3s3n 3s3o 4bac 4bdy 4bdz 4be0 4be1 4be2 4e7h 4e7i 4e7k 4e7l 4ikf 4ztf 4ztj 5frm 5frn 5fro 5uop 5uoq

(-) Related Entries Specified in the PDB File

3dlr CATALYTIC CORE DOMAIN OF THE SAME PROTEIN
3os2 SAME COMPLEX AT A LOWER RESOLUTION
3oy9 VIRAL DNA - INTEGRASE COMPLEX PRIOR TO BINDING TARGET DNA
3oya VIRAL DNA - INTEGRASE COMPLEX PRIOR TO BINDING TARGET DNA, INHIBITED BY RALTEGRAVIR