Structure of PDB 7ykn Chain A Binding Site BS01

Receptor Information
>7ykn Chain A (length=507) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYSVVRLILGDQLNHAHSWFSEHRDDVLYLIAELHQEQEYVRHHIQKQCA
FFAAMQAFADYLSAEGHHVWHLDLDASAQYNDLPDLIAQICQQVQADAFQ
YQRPDEYRLLEQMANLRLSGITIGCVDTEHFLLPFAEIPEQFPASKAVLM
EHFYRRMRKRFGYLMTADGKPEGGQWNFDADNRNKLKSPDLLQLPTPLCF
DNPVASIKARIERHRIPSIGQVGESLLWPINRAQALSLLAHFCQICLPNF
GRFQDAMTAQHPHRWSLYHSRLSFALNSKLLSPREVIEATISAYRAAQGQ
ISLAQVEGFVRQILGWREYVRGMYWSNMPHYQTRNHLGAQRPLPSYFWNG
QTKMRCLQQAITQSLDFGYAHHIQRLMVTGNFALLTECDPDQVDAWYLGI
YIDAIEWVELPNTRGMALFADGGLIATKPYSASGSYINKMSDYCASCAYQ
VKLKSGEKACPLNSLYWRFMLKHRDRMLYKTWDKMTSDSQQAILSTADAY
LSQIESL
Ligand information
Ligand IDDLZ
InChIInChI=1S/C13H18N4O6/c1-5-6(2)17(3-7(19)10(21)8(20)4-18)11-9(14-5)12(22)16-13(23)15-11/h7-8,10,18-21H,3-4H2,1-2H3,(H,16,22,23)/t7-,8+,10-/m0/s1
InChIKeySXDXRJZUAJBNFL-XKSSXDPKSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C2N=C1N(C(=C(N=C1C(=O)N2)C)C)CC(O)C(O)C(O)CO
OpenEye OEToolkits 1.5.0CC1=C(N(C2=NC(=O)NC(=O)C2=N1)C[C@@H]([C@@H]([C@@H](CO)O)O)O)C
CACTVS 3.341CC1=C(C)N(C[CH](O)[CH](O)[CH](O)CO)C2=NC(=O)NC(=O)C2=N1
OpenEye OEToolkits 1.5.0CC1=C(N(C2=NC(=O)NC(=O)C2=N1)CC(C(C(CO)O)O)O)C
CACTVS 3.341CC1=C(C)N(C[C@H](O)[C@H](O)[C@H](O)CO)C2=NC(=O)NC(=O)C2=N1
FormulaC13 H18 N4 O6
Name1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol;
6,7-dimethyl-8-(1'-D-ribityl) lumazine
ChEMBL
DrugBank
ZINCZINC000004096380
PDB chain7ykn Chain A Residue 603 [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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PDB7ykn The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
G11 D12 E34 L35 E38 Q39 Y41 F52 M56 D106 L110 I406
Binding residue
(residue number reindexed from 1)
G10 D11 E33 L34 E37 Q38 Y40 F51 M55 D105 L109 I405
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding

View graph for
Molecular Function
External links
PDB RCSB:7ykn, PDBe:7ykn, PDBj:7ykn
PDBsum7ykn
PubMed36528063
UniProtA0A2V4NVF4

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