Structure of PDB 8j2w Chain B Binding Site BS01

Receptor Information
>8j2w Chain B (length=329) Species: 103733 (Saccharothrix syringae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DILAAGREELMAALAEGDEHAAVDLAMRLLDGGVPADVVLLELVADAQVE
IGVLWQANRWSVAQEHAATAISERVIAAVGDRAAAAPTRGHVVVACLDGE
WHALPARIVAEVLRGRGWRVTFLGASVPAAHLVPYLEEHGPDAVALSCTL
PRGLPRADQVVAACRATGTPVLVGGLGFGPDGRWARVLGAGTWAPTARAA
ADLLDRPERPADPEYAALRARRAELVDAGLAALHEWFPPLRDYDARRLDA
TLDDLGDIVDHLAASVYVDDPELFGEFVTWTAEVLAARGVSPASVEVALE
AIARVLDDHPRTRHHLDHGRRALAAHLEH
Ligand information
Ligand IDB12
InChIInChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
InChIKeyLKVIQTCSMMVGFU-DWSMJLPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C](C)([CH]8N|3=C(C(=C4[CH](CCC(N)=O)C5(C)C)C)[C](C)(CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[CH]8CC(N)=O)[C](C)(CC(N)=O)[CH]7CCC(N)=O)[C](C)(CC(N)=O)[CH]6CCC(N)=O
CACTVS 3.370[Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C@@](C)([C@@H]8N|3=C(C(=C4[C@@H](CCC(N)=O)C5(C)C)C)[C@](C)(CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[C@H]8CC(N)=O)[C@@](C)(CC(N)=O)[C@@H]7CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O
FormulaC62 H89 Co N13 O14 P
NameCOBALAMIN
ChEMBL
DrugBank
ZINC
PDB chain8j2w Chain B Residue 403 [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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PDB8j2w Photocobilins integrate B12 and bilin photochemistry for enzyme control.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
A51 Q54 G58 Q62 E71 T75 W107 H108 A109 L110 P111 V115 A151 L152 S153 L156 L178 V179 G180 G181 A200 P201 T202 A203 W296
Binding residue
(residue number reindexed from 1)
A45 Q48 G52 Q56 E65 T69 W101 H102 A103 L104 P105 V109 A145 L146 S147 L150 L172 V173 G174 G175 A194 P195 T196 A197 W280
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0031419 cobalamin binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:8j2w, PDBe:8j2w, PDBj:8j2w
PDBsum8j2w
PubMed38548733
UniProtA0A5Q0H231

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