Structure of PDB 2vf8 Chain A Binding Site BS02

Receptor Information
>2vf8 Chain A (length=806) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYA
EAQRRYLESVSPYARRLFNQVPDVDAIDGLPPAVALQQARGTPTARSSVG
SVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVY
TVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWREL
PEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRH
VLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITE
LSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLD
VLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAG
LHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKG
GEILYSGPPEGLKHVPESQTGQYLFADEPHTPREPAGWLELNGVTRNNLD
NLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQGSARLGGDLA
QITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGR
FSFNVKGGRCEHCQGEGWVMVPSVYAPCPVCHGTRYNAETLEVEYRGKNI
ADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEA
QRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTV
IAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPY
LRAALR
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2vf8 Chain A Residue 1844 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2vf8 Structural and Mutational Analyses of Deinococcus Radiodurans Uvra2 Provide Insight Into DNA Binding and Damage Recognition by Uvras.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		Y370 R375 N511 N512 G533 G535 K536 S537 T538
Binding residue
(residue number reindexed from 1)		Y359 R364 N497 N498 G519 G521 K522 S523 T524
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004518 nuclease activity
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
Cellular Component
GO:0005737 cytoplasm
GO:0009380 excinuclease repair complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2vf8, PDBe:2vf8, PDBj:2vf8
PDBsum2vf8
PubMed19368888
UniProtQ9RYW8

[Back to BioLiP]