Structure of PDB 2d7d Chain A Binding Site BS02

Receptor Information
>2d7d Chain A (length=621) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DRFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNL
IKEVNKPTLVIAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYV
PQTDTFIEKDASINDEIDKLRHSATSALFERRDVIIIASVSCIYGLGSPE
EYREMVVSLRTEMEIERNELLRKLVDIQYARNDIDFQRGTFRVRGDVVEI
FPASRDEHCVRVEFFGDEIERIREVDALTGEILGDRDHVAIFPASHFVTR
AEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGF
CSGIENYSRHLTLRPPGSTPYTLLDYFPDDFMIVVDESHVTIPQVRGMFN
GDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYVSATPGPYEIE
HTDEMVEQIIRPTGLLDPLIDVRPIEGQIDDLIGEIQARIERNERVLVTT
LTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGI
NLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIMY
ADKITKSMEIAINETKRRREQQERFNEEHGITPKTINKKERQKVVEQMEH
EMKEAAKALDFERAAELRDLL
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 chain2d7d Chain A Residue 662 [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]
PDB2d7d Structural insights into the cryptic DNA-dependent ATPase activity of UvrB
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y11 Q12 Q14 Q17 G42 T43 G44 K45 F47 P414 R543
Binding residue
(residue number reindexed from 1)		Y9 Q10 Q12 Q15 G40 T41 G42 K43 F45 P412 R541
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.-.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004518 nuclease activity
GO:0005524 ATP binding
GO:0009381 excinuclease ABC activity
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0009432 SOS response
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:2d7d, PDBe:2d7d, PDBj:2d7d
PDBsum2d7d
PubMed16426634
UniProtP37954|UVRB_BACSU UvrABC system protein B (Gene Name=uvrB)

[Back to BioLiP]