Structure of PDB 1bmt Chain A Binding Site BS01

Receptor Information
>1bmt Chain A (length=246) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDG
MNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMV
IATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADL
IGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNY
SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGR
Ligand information
Ligand IDCOB
InChIInChI=1S/C62H88N13O14P.CH3.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;;/h20-21,23,28,31,34-37,41,52-53,57,76,84H,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);1H3;/q;;+1/b42-23-,54-32-,55-33-;;/t31-,34-,35-,36-,37+,41-,52-,53-,57+,59-,60+,61+,62+;;/m1../s1
InChIKeyBMOGZGJBQIUQJG-BYLSPCLQSA-N
SMILES
SoftwareSMILES
Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@@](=O)(O)O[C@H](C)CNC(=O)CC[C@@]4([C@H](C5=[N-]6C4=C(C7=[N]8[Co+2]69([N]1=C(C=C8C([C@@H]7CCC(=O)N)(C)C)[C@H]([C@](C1=C(C1=[N]9[C@@]5([C@@]([C@@H]1CCC(=O)N)(C)CC(=O)N)C)C)(C)CC(=O)N)CCC(=O)N)C)C)CC(=O)N)C)O
C[Co++]|12|3|N4=C5C=C6N|1=C([CH](CCC(N)=O)C6(C)C)C(=C7[N-]2=C([CH](CC(N)=O)[C]7(C)CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]8[CH](O)[CH](O[CH]8CO)n9cnc%10cc(C)c(C)cc9%10)[C]%11(C)N|3=C([CH](CCC(N)=O)[C]%11(C)CC(N)=O)C(=C4[C](C)(CC(N)=O)[CH]5CCC(N)=O)C)C
OpenEye OEToolkits 1.7.5Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5=[N-]6C4=C(C7=[N]8[Co+2]69([N]1=C(C=C8C(C7CCC(=O)N)(C)C)C(C(C1=C(C1=[N]9C5(C(C1CCC(=O)N)(C)CC(=O)N)C)C)(C)CC(=O)N)CCC(=O)N)C)C)CC(=O)N)C)O
C[Co++]|12|3|N4=C5C=C6N|1=C([C@@H](CCC(N)=O)C6(C)C)C(=C7[N@@-]2=C([C@H](CC(N)=O)[C@@]7(C)CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]8[C@@H](O)[C@H](O[C@@H]8CO)n9cnc%10cc(C)c(C)cc9%10)[C@]%11(C)N|3=C([C@@H](CCC(N)=O)[C@]%11(C)CC(N)=O)C(=C4[C@@](C)(CC(N)=O)[C@@H]5CCC(N)=O)C)C
FormulaC63 H91 Co N13 O14 P
NameCO-METHYLCOBALAMIN
ChEMBL
DrugBank
ZINC
PDB chain1bmt Chain A Residue 122 [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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PDB1bmt How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		E694 M698 M701 G705 L715 V718 D757 V758 H759 D760 I761 I765 G802 L803 S804 L806 I807 T808 G833 G834 A835 V857 N859 A860
Binding residue
(residue number reindexed from 1)		E44 M48 M51 G55 L65 V68 D107 V108 H109 D110 I111 I115 G152 L153 S154 L156 I157 T158 G183 G184 A185 V207 N209 A210
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D757 H759 S810
Catalytic site (residue number reindexed from 1) D107 H109 S160
Enzyme Commision number 2.1.1.13: methionine synthase.
Gene Ontology
Molecular Function
GO:0031419 cobalamin binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:1bmt, PDBe:1bmt, PDBj:1bmt
PDBsum1bmt
PubMed7992050
UniProtP13009|METH_ECOLI Methionine synthase (Gene Name=metH)

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