Structure of PDB 8oya Chain B Binding Site BS03

Receptor Information
>8oya Chain B (length=417) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIRALKSGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDEF
LEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKDYNAG
TLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAH
TFRPKLYALLPEFLEEFPELEPNSVTDPLFEPWHFEPGEKAAKKVMESFI
ADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSK
KAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIY
TLEEFEAGKTHDPLWNASQMELLSTGKMHGYMRMYWAKKILEWSESPEKA
LEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSY
EGCKRKFDVKLYIEKYS
Ligand information
Ligand IDFDA
InChIInChI=1S/C27H35N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyYPZRHBJKEMOYQH-UYBVJOGSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C3C=2Nc1cc(c(cc1N(C=2NC(=O)N3)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
FormulaC27 H35 N9 O15 P2
NameDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000095099885
PDB chain8oya Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8oya Time-resolved crystallography captures light-driven DNA repair
Resolution2.18 Å
Binding residue
(original residue number in PDB)		Y252 L264 S265 N266 S268 F298 E301 W305 K306 K372 G375 R378 N403 D409 N414 G415 G418
Binding residue
(residue number reindexed from 1)		Y207 L219 S220 N221 S223 F253 E256 W260 K261 K327 G330 R333 N358 D364 N369 G370 G373
Annotation score1
Enzymatic activity
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
Biological Process
GO:0000719 photoreactive repair
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8oya, PDBe:8oya, PDBj:8oya
PDBsum8oya
PubMed38033070
UniProtQ8PYK9

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