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 (PFV) INTASOME IN COMPLEX WITH MAGNESIUM AND THE INSTI XZ384 (COMPOUND 4A)
 
Authors :  D. P. Maskell, V. E. Pye, P. Cherepanov
Date :  18 Dec 15  (Deposition) - 17 Feb 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Recombination, Viral Protein/Dna, Protein-Dna Complex, Tetramer, Dna Integration, Endonuclease, Metal-Binding, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Nucleus, Transferase, Viral Nucleoprotein, Virion, Dna- Binding, Zinc Binding, Hhcc Motif, Viral Protein, Inhibitor, Dna-Binding Protein-Dna Complex, (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Z. Zhao, S. J. Smith, D. P. Maskell, M. Metifiot, V. E. Pye, K. Fesen, C. Marchand, Y. Pommier, P. Cherepanov, S. H. Hughes, T. R. J. Burke
Hiv-1 Integrase Strand Transfer Inhibitors With Reduced Susceptibility To Drug Resistant Mutant Integrases.
Acs Chem. Biol. V. 11 1074 2016
PubMed-ID: 26808478  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00948

(-) Compounds

Molecule 1 - PFV INTEGRASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LinePC2
    Expression System PlasmidPSSH6P-PFV-INFL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificHUMAN SPUMARETROVIRUS
    Organism Taxid11963
    StrainHSRV2
    SynonymPRO-POL POLYPROTEIN PR125POL, P87PRO-RT-RNASEH, P65PRO-RT, P42IN, PFV INTEGRASE
    VariantPOL
 
Molecule 2 - 5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP *TP*CP*GP*CP*A)-3'
    ChainsC
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP *AP*CP*A)-3'
    ChainsD
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION
4SO45Ligand/IonSULFATE ION
5WA51Ligand/Ion4-AZANYLIDENE-N-[[2,4-BIS(FLUORANYL)PHENYL]METHYL]-1-OXIDANYL-2-OXIDANYLIDENE-1,8-NAPHTHYRIDINE-3-CARBOXAMIDE
6ZN1Ligand/IonZINC ION
Biological Unit 1 (4, 30)
No.NameCountTypeFull Name
1GOL16Ligand/IonGLYCEROL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4SO410Ligand/IonSULFATE ION
5WA52Ligand/Ion4-AZANYLIDENE-N-[[2,4-BIS(FLUORANYL)PHENYL]METHYL]-1-OXIDANYL-2-OXIDANYLIDENE-1,8-NAPHTHYRIDINE-3-CARBOXAMIDE
6ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:62 , HIS A:66 , CYS A:96 , CYS A:99BINDING SITE FOR RESIDUE ZN A1376
02AC2SOFTWAREASP A:128 , ASP A:185 , HOH A:2027 , HOH A:2028 , WA5 D:1018BINDING SITE FOR RESIDUE MG A1377
03AC3SOFTWAREASP A:128 , GLU A:221 , HOH A:2029 , WA5 D:1018BINDING SITE FOR RESIDUE MG A1378
04AC4SOFTWARELYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260BINDING SITE FOR RESIDUE SO4 B1299
05AC5SOFTWAREASP A:128 , ASP A:185 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:1377 , MG A:1378 , MES A:1380 , SO4 A:1383 , HOH A:2028 , DG C:4 , DC D:16 , DA D:17BINDING SITE FOR RESIDUE WA5 D1018
06AC6SOFTWAREPRO A:135 , SER A:136 , GLN A:137 , LYS A:241BINDING SITE FOR RESIDUE SO4 A1379
07AC7SOFTWAREGLN A:186 , GLY A:187 , PRO A:211 , TYR A:212 , SO4 A:1383 , WA5 D:1018BINDING SITE FOR RESIDUE MES A1380
08AC8SOFTWARESER A:225 , THR A:232 , ARG A:336 , HOH A:2017 , DC D:16BINDING SITE FOR RESIDUE GOL A1381
09AC9SOFTWAREGLN A:60 , LEU A:79 , TYR A:80 , PRO A:277 , PHE A:278BINDING SITE FOR RESIDUE GOL A1382
10BC1SOFTWAREGLY A:187 , ALA A:188 , MES A:1380 , DA D:17 , WA5 D:1018BINDING SITE FOR RESIDUE SO4 A1383
11BC2SOFTWARELYS A:228 , SER A:332 , LEU A:333 , ARG A:336BINDING SITE FOR RESIDUE SO4 A1384
12BC3SOFTWAREHIS A:338 , LYS A:339 , HIS A:357BINDING SITE FOR RESIDUE SO4 A1385
13BC4SOFTWARETHR A:163 , SER A:164 , HOH A:2037BINDING SITE FOR RESIDUE GOL A1386
14BC5SOFTWARELEU A:292 , GLN A:296 , TYR B:263 , GLY B:271 , ASP B:273BINDING SITE FOR RESIDUE GOL B1300
15BC6SOFTWAREASP A:116 , DT C:3BINDING SITE FOR RESIDUE GOL A1387
16BC7SOFTWARETYR A:303 , GOL A:1388 , HOH A:2067 , DC C:6 , DA C:7 , DT C:8 , DC D:11BINDING SITE FOR RESIDUE GOL C1020
17BC8SOFTWARESER A:175 , LEU B:155 , PRO B:157 , TYR B:243 , PRO B:247 , GLN B:250BINDING SITE FOR RESIDUE GOL B1301
18BC9SOFTWAREARG A:114 , TYR A:303 , PRO A:305 , HOH A:2095 , DC C:6 , GOL C:1020BINDING SITE FOR RESIDUE GOL A1388

(-) SS Bonds  (0, 0)

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

(-) 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 5FRM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FRM)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...........eeee..eeeeee..eeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh....ee..............eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhhhh............ee......eeee...............eeeeeeee..eeeee.....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frm A   9 DAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 375
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       

Chain B from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frm B 116 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEI 298
                                   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
                                                   
                 5frm C   1 ATTGTCATGGAATTTCGCA  19
                                    10         

Chain D from PDB  Type:DNA  Length:17
                                                 
                 5frm 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 5FRM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    WA5  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5frm
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POL_FOAMV | P14350
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  POL_FOAMV | P14350
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POL_FOAMV | P143502lsn 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 4ztf 4ztj 5frn 5fro 5uop 5uoq

(-) Related Entries Specified in the PDB File

5frn CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS (PFV) INTASOME IN COMPLEX WITH MAGNESIUM AND THE INSTI XZ419 (COMPOUND 4C)
5fro CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS (PFV) INTASOME IN COMPLEX WITH MAGNESIUM AND THE INSTI XZ446 (COMPOUND 4F)