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(-) Description

Title :  PFV INTASOME WITH INHIBITOR MB-76
 
Authors :  O. Taltynov, J. Demeulemeester, B. A. Desimmie, V. Suchaud, M. Billamb C. Lion, F. Bailly, Z. Debyser, P. Cotelle, F. Christ, S. V. Strelkov
Date :  26 Dec 12  (Deposition) - 03 Apr 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Integrase Zinc Binding, Core And Dna-Binding Domains, Dna Integration, Inhibitor, Nucleus, Viral Protein-Dna-Inhibitor Complex, Endonuclease, Nucleotidyltransferase, Recombination, Hhcc Motif, Dde Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Desimmie, J. Demeulemeester, V. Suchaud, O. Taltynov, M. Billamboz, C. Lion, F. Bailly, S. V. Strelkov, Z. Debyser, P. Cotelle, F. Christ
2-Hydroxyisoquinoline-1, 3(2H, 4H)-Diones (Hids), Novel Inhibitors Of Hiv Integrase With A High Barrier To Resistance.
Acs Chem. Biol. V. 8 1187 2013
PubMed-ID: 23517458  |  Reference-DOI: 10.1021/CB4000426

(-) Compounds

Molecule 1 - INTEGRASE
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS (DE3)
    Expression System Taxid: 469008
    Gene: POL
    Organism Common: SFVCPZ(HU)
    Organism Scientific: HUMAN SPUMARETROVIRUS
    Organism Taxid: 11963
    Strain: HSRV2
    Synonym: IN, P42IN
 
Molecule 2 - 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: PFV LTR 5' END
    Synthetic: YES
 
Molecule 3 - 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: PFV LTR 3' END
    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  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HEZ1Ligand/IonHEXANE-1,6-DIOL
3M761Ligand/IonN-(4-FLUOROBENZYL)-2,3-DIHYDROXY-1-OXO-1,2-DIHYDROISOQUINOLINE-4-CARBOXAMIDE
4MG2Ligand/IonMAGNESIUM ION
5NH41Ligand/IonAMMONIUM ION
6SO42Ligand/IonSULFATE ION
7ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 18)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2HEZ2Ligand/IonHEXANE-1,6-DIOL
3M762Ligand/IonN-(4-FLUOROBENZYL)-2,3-DIHYDROXY-1-OXO-1,2-DIHYDROISOQUINOLINE-4-CARBOXAMIDE
4MG-1Ligand/IonMAGNESIUM ION
5NH42Ligand/IonAMMONIUM ION
6SO44Ligand/IonSULFATE ION
7ZN-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
02AC2SOFTWAREHIS A:338 , LYS A:339 , HIS A:357BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREASP A:116 , DT C:3BINDING SITE FOR RESIDUE NH4 A 403
04AC4SOFTWAREASP A:128 , ASP A:185 , M76 D:101BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWAREASP A:128 , GLU A:221 , ASN A:224 , M76 D:101BINDING SITE FOR RESIDUE MG A 405
06AC6SOFTWARESER A:162 , THR A:163 , SER A:164 , ALA A:188BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREPRO A:135 , SER A:136 , GLN A:137 , THR A:240 , LYS A:241BINDING SITE FOR RESIDUE GOL A 407
08AC8SOFTWAREGLN A:60 , LEU A:79 , TYR A:80 , PRO A:277 , PHE A:278BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWARETYR B:263 , GLN B:267 , GLY B:271 , ILE B:272 , ASP B:273BINDING SITE FOR RESIDUE GOL B 401
10BC1SOFTWARELYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260BINDING SITE FOR RESIDUE SO4 B 402
11BC2SOFTWAREVAL A:172 , LEU B:155 , TYR B:156 , TYR B:243 , PRO B:247 , GLN B:250BINDING SITE FOR RESIDUE HEZ B 403
12BC3SOFTWAREASP A:128 , ASP A:185 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:404 , MG A:405 , DG C:4 , DC D:16 , DA D:17BINDING SITE FOR RESIDUE M76 D 101

(-) SS Bonds  (0, 0)

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

(-) 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 4IKF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IKF)

(-) 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 ...hhhhhhhh....................eee..eee...hhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhh....ee..............eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh........hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh............ee......eeee...............eee.......eeeeee....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ikf 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 ........eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh........hhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ikf 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
                                                   
                 4ikf C   1 ATTGTCATGGAATTTCGCA  19
                                    10         


Chain D from PDB  Type:DNA  Length:17
                                                 
                 4ikf 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 4IKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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        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 4ztf 4ztj 5frm 5frn 5fro 5uop 5uoq

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