Structure of PDB 3iv9 Chain A Binding Site BS01

Receptor Information
>3iv9 Chain A (length=577) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPCEVIEGPLMDG
MNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQCKTNGKMV
IATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADL
IGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNY
SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR
TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPF
FMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVG
LFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKTGFANYCLADFVAPK
LSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFA
EYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKAT
IWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV
EDYARRKGMSVTEVERWLAPNLGYDAD
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 chain3iv9 Chain A Residue 1301 [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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PDB3iv9 Insights into the reactivation of cobalamin-dependent methionine synthase.
Resolution3.25 Å
Binding residue
(original residue number in PDB)		V758 H759 I761 G762 I765 G802 S804 L806 T808 G833 G834 A835 V857 Q858 N859 A860 D1093 P1137 G1138 Y1139 H1145 M1171 G1174 A1175 S1176 V1177 S1178
Binding residue
(residue number reindexed from 1)		V108 H109 I111 G112 I115 G152 S154 L156 T158 G183 G184 A185 V207 Q208 N209 A210 D443 P487 G488 Y489 H495 M521 G524 A525 S526 V527 S528
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:0008705 methionine synthase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
Biological Process
GO:0009086 methionine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3iv9, PDBe:3iv9, PDBj:3iv9
PDBsum3iv9
PubMed19846791
UniProtP13009|METH_ECOLI Methionine synthase (Gene Name=metH)

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