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 :  CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2-PYRIDINONE AMINAL INHIBITOR
 
Authors :  D. J. Klein, S. Patel
Date :  14 May 15  (Deposition) - 07 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Transferase-Dna Complex, Dna Integration, Viral Protein, Recombination-Inhibitor-Dna Complex, Transferase-Dna-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. T. Raheem, A. M. Walji, D. Klein, J. M. Sanders, D. A. Powell, P. Abeywickrema, G. Barbe, A. Bennet, S. D. Clas, D. Dubost, M. Embrey, J. Grobler, M. J. Hafey, T. J. Hartingh, D. J. Hazuda, M. D. Miller, K. P. Moore, N. Pajkovic, S. Patel, V. Rada, P. Rearden, J. D. Schreier, J. Sisko, T. G. Steele, J. F. Truchon, J. Wai, M. Xu, P. J. Coleman
Discovery Of 2-Pyridinone Aminals: A Prodrug Strategy To Advance A Second Generation Of Hiv-1 Integrase Strand Transfer Inhibitors.
J. Med. Chem. V. 58 8154 2015
PubMed-ID: 26397965  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01037

(-) Compounds

Molecule 1 - INTEGRASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POL
    Organism Common: SFVCPZ(HU)
    Organism Scientific: HUMAN SPUMARETROVIRUS
    Organism Taxid: 11963
    Synonym: PR125POL
 
Molecule 2 - 19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
    Chains: C
    Engineered: YES
    Organism Scientific: HUMAN SPUMARETROVIRUS
    Organism Taxid: 11963
    Synthetic: YES
 
Molecule 3 - 17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
    Chains: D
    Engineered: YES
    Organism Scientific: HUMAN SPUMARETROVIRUS
    Organism Taxid: 11963
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG3Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION
4X2P1Ligand/Ion(1R,2R,5S)-8'-(3-CHLORO-4-FLUOROBENZYL)-6'-HYDROXY-2'-[(2S)-2-HYDROXYPROPYL]-9',10'-DIHYDRO-2'H-SPIRO[BICYCLO[3.1.0]HEXANE-2,3'-IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE]-1',5',7'(8'H)-TRIONE
5ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO46Ligand/IonSULFATE ION
4X2P2Ligand/Ion(1R,2R,5S)-8'-(3-CHLORO-4-FLUOROBENZYL)-6'-HYDROXY-2'-[(2S)-2-HYDROXYPROPYL]-9',10'-DIHYDRO-2'H-SPIRO[BICYCLO[3.1.0]HEXANE-2,3'-IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE]-1',5',7'(8'H)-TRIONE
5ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:62 , HIS A:66 , CYS A:96 , CYS A:99binding site for residue ZN A 401
02AC2SOFTWARESER A:162 , THR A:163 , SER A:164 , HOH A:506binding site for residue GOL A 402
03AC3SOFTWAREPRO A:135 , SER A:136 , GLN A:137 , LYS A:241binding site for residue GOL A 403
04AC4SOFTWAREASP A:128 , ASP A:185 , GLY A:187 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:405 , MG A:406 , HOH A:549 , DG C:4 , DC D:16 , DA D:17 , HOH D:101binding site for residue X2P A 404
05AC5SOFTWAREASP A:128 , ASP A:185 , X2P A:404 , HOH A:521 , HOH A:549binding site for residue MG A 405
06AC6SOFTWAREASP A:128 , GLU A:221 , X2P A:404 , HOH D:101binding site for residue MG A 406
07AC7SOFTWARELYS A:228 , SER A:332 , LEU A:333 , ARG A:336 , HOH A:518 , DA D:17binding site for residue SO4 A 407
08AC8SOFTWAREHIS A:338 , LYS A:339 , HIS A:357 , HOH A:544binding site for residue SO4 A 408
09AC9SOFTWARELEU A:292 , GLN A:296 , TYR B:263binding site for residue GOL A 409
10AD1SOFTWARELYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260binding site for residue SO4 B 401
11AD2SOFTWAREASP B:128 , ASP B:185 , DA C:19binding site for residue MG B 402
12AD3SOFTWARETYR A:303 , DC C:6 , DA C:7 , DT C:8 , HOH C:203 , HOH C:212 , HOH C:216 , DC D:11binding site for residue GOL C 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:131 -Pro A:132
2Gly B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZTF)

(-) 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:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...........eeee..eeeeee..eeee..hhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhhhh.hhhhhhhh....ee..............eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhhhh............ee......eeee...............eeeeeeee..eeeee.....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztf A   8 LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 375
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztf B 116 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIR 299
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    


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


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4ztf D   1 TGCGAAATTCCATGACA  17
                                    10
   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 4ZTF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    X2P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:131 - Pro A:132   [ RasMol ]  
    Gly B:131 - Pro B:132   [ 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
  4ztf
    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)
  (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_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 4e7j 4e7k 4e7l 4ikf 4ztj 5frm 5frn 5fro 5uop 5uoq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZTF)