Structure of PDB 2r6f Chain A Binding Site BS01

Receptor Information
>2r6f Chain A (length=899) Species: 272567 (Geobacillus stearothermophilus 10) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDKIIVKGARAHNLKNIDVEIPRGKLVVLTGLSGSGKSSLAFDTIYAEGQ
RRYVESLSAYARQFLGQMEKPDVDAIEGLSPAISIDQKTTSRNPRSTVGT
VTEIYDYLRLLFARIGRPICPTHGIEIQSQTIEQMVDRLLSYPERTKMQI
LAPIDVVVDRIIIKDGIAARLADSLETALKLADGKVVVDVIGEGELLFSE
KHACPYCGFSIGELEPRLFSFNSPFGACPDCDGLGAKLEVDLDLVIPNDE
LTLKEHAIAPWEPYYPQLLEAVCRHYGIPMDVPVKDLPKEQLDKILYGSG
GEPIYFRYTNDFGQVREQYIAFEGVIPNVERRYRETSSDYIREQMEKYMA
EQPCPTCQGYRLKKESLAVLVGGKHIGEVTAMSVTEALAFFDGLELTEKE
AQIARLILREIRDRLGFLQNVGLDYLTLSRSAGTLSGGEAQRIRLATQIG
SRLTGVLYVLDEPSIGLHQRDNDRLIATLKSMRDLGNTLIVVEHDEDTML
AADYLIDIGPGAGIHGGEVVAAGTPEEVMNDPNSLTGQYLSGKKFIPIPA
ERRRPDGRWLEVVGAREHNLKNVSVKIPLGTFVAVTGVSGSGKSTLVNEV
LYKALAQKLHRAKAKPGEHRDIRGLEHLDKVIDIDQSPIGRTPRSNPATY
TGVFDDIRDVFASTNEAKVRGYKKGRFSFNVKGGRCEACHGDGIIKIEMH
FLPDVYVPCEVCHGKRYNRETLEVTYKGKNIAEVLDMTVEDALDFFASIP
KIKRKLETLYDVGLGYMKLGQPATTLSGGEAQRVKLAAELHRRSNGRTLY
ILDEPTTGLHVDDIARLLDVLHRLVDNGDTVLVIEHNLDVIKTADYIIDL
GPEGGDRGGQIVAVGTPEEVAEVKESHTGRYLKPILERDRARMQARYEA
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 chain2r6f Chain A Residue 1000 [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]
PDB2r6f Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		H12 N13 G34 S35 G36 K37 S38 S39 Y816 Q821
Binding residue
(residue number reindexed from 1)		H12 N13 G34 S35 G36 K37 S38 S39 Y766 Q771
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=8.00,Kd=10nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0004518 nuclease activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0009381 excinuclease ABC activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
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:2r6f, PDBe:2r6f, PDBj:2r6f
PDBsum2r6f
PubMed18158267
UniProtQ5KVB6

[Back to BioLiP]