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Structure of PDB 2vf8 Chain B Binding Site BS01

Receptor Information

>2vf8 Chain B (length=835) Species: 1299 (Deinococcus radiodurans)

PDFPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTL
YAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTAR
SSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGL
GRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVP
WRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSS
ARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGL
DITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLV
KRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDE
PSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEA
GEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNG
VTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQPVN
PDPEDDEDPADHTAGSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTG
LFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFL
PSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAI
FRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVL
DEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGP
GAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR

Ligand information

• Ligand ID: ADP
• InChI: InChI=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
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 2vf8 Chain B Residue 1843

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vf8 Structural and Mutational Analyses of Deinococcus Radiodurans Uvra2 Provide Insight Into DNA Binding and Damage Recognition by Uvras.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): H24 N25 G46 S47 G48 K49 S50 S51 R101 Q726 E730
• Binding residue (residue number reindexed from 1): H17 N18 G39 S40 G41 K42 S43 S44 R94 Q719 E723
• Annotation score: 5

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

External links

• PDB: RCSB:2vf8, PDBe:2vf8, PDBj:2vf8
• PDBsum: 2vf8
• PubMed: 19368888
• UniProt: Q9RYW8

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