Structure of PDB 2j08 Chain A Binding Site BS02

Receptor Information
>2j08 Chain A (length=419) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFL
ENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYG
RYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLP
PPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEER
DRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFS
YHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRE
LHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGW
QWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVV
DLEEARRRYLRLARDLARG
Ligand information
Ligand IDIRF
InChIInChI=1S/C16H17IN4O6/c1-6-2-8-9(3-7(6)17)21(4-10(23)13(25)11(24)5-22)14-12(18-8)15(26)20-16(27)19-14/h2-3,10-11,13,22-25H,4-5H2,1H3,(H,20,26,27)/t10-,11+,13-/m0/s1
InChIKeyGXUZMSUHTJJUNU-LOWVWBTDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO)c2cc1I
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1I)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1I
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1I)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO)O)O)O
ACDLabs 10.04Ic2cc1N(C3=NC(=O)NC(=O)C3=Nc1cc2C)CC(O)C(O)C(O)CO
FormulaC16 H17 I N4 O6
Name1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL;
8-IODO-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)
ChEMBL
DrugBank
ZINCZINC000034951247
PDB chain2j08 Chain A Residue 1422 [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]
PDB2j08 Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus
Resolution2.61 Å
Binding residue
(original residue number in PDB)
R9 G10 V34 N39 R46 F50 S96 R104 L218
Binding residue
(residue number reindexed from 1)
R8 G9 V33 N38 R45 F49 S95 R103 L217
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E244 W247 W275 N310 W328 W351
Catalytic site (residue number reindexed from 1) E243 W246 W274 N309 W327 W350
Enzyme Commision number 4.1.99.3: deoxyribodipyrimidine photo-lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003904 deoxyribodipyrimidine photo-lyase activity
GO:0016829 lyase activity
GO:0071949 FAD binding
GO:0097159 organic cyclic compound binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006950 response to stress
GO:0009416 response to light stimulus

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:2j08, PDBe:2j08, PDBj:2j08
PDBsum2j08
PubMed17051659
UniProtP61497|PHR_THET8 Deoxyribodipyrimidine photo-lyase (Gene Name=phr)

[Back to BioLiP]