Structure of PDB 7yd6 Chain A Binding Site BS03

Receptor Information
>7yd6 Chain A (length=456) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEA
NVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPETLSDVLET
GVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALR
NDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWK
EISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTH
DPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRY
ELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKL
YIEKYS
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/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/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(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
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)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
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(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
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain7yd6 Chain A 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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PDB7yd6 Visualizing the DNA repair process by a photolyase at atomic resolution
Resolution2.15 Å
Binding residue
(original residue number in PDB)		Y252 S265 N266 S268 F298 E301 I302 W305 K372 R378 N403 D409 N414 G415
Binding residue
(residue number reindexed from 1)		Y246 S259 N260 S262 F292 E295 I296 W299 K366 R372 N397 D403 N408 G409
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:7yd6, PDBe:7yd6, PDBj:7yd6
PDBsum7yd6
PubMed38033054
UniProtQ8PYK9

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