Structure of PDB 1y80 Chain A Binding Site BS01

Receptor Information
>1y80 Chain A (length=125) Species: 1525 (Moorella thermoacetica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPSVGKIVLGTVKGDLHDIGKNLVAMMLESGGFTVYNLGVDIEPGKFVEA
VKKYQPDIVGMSALLTTTMMNMKSTIDALIAAGLRDRVKVIVGGAPLSQD
FADEIGADGYAPDAASATELCRQLL
Ligand information
Ligand IDB1M
InChIInChI=1S/C61H86N13O15P.Co/c1-29(88-90(84,85)89-52-40(27-75)87-56(51(52)83)74-28-69-38-21-32(86-10)11-15-39(38)74)26-68-48(82)19-20-58(6)36(22-45(65)79)55-61(9)60(8,25-47(67)81)35(14-18-44(64)78)50(73-61)31(3)54-59(7,24-46(66)80)33(12-16-42(62)76)37(70-54)23-41-57(4,5)34(13-17-43(63)77)49(71-41)30(2)53(58)72-55;/h11,15,21,23,28-29,33-36,40,51-52,56,75,83-84H,12-14,16-20,22,24-27H2,1-10H3,(H2,62,76)(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H,68,82);/q-1;+4/b41-23-,53-30-,54-31-;/t29-,33-,34-,35-,36+,40-,51-,52-,56+,58-,59+,60+,61+;/m1./s1
InChIKeyCJVUSTVYODMZMZ-VSTXFNHGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1=C2C(C(C3=[N+]2[Co]45[N+]6=C1C(C(C6=CC7=[N+]4C(=C(C8=[N+]5C3(C(C8CCC(=O)N)(C)CC(=O)N)C)C)C(C7CCC(=O)N)(C)CC(=O)N)(C)C)CCC(=O)N)CC(=O)N)(C)CCC(=O)NCC(C)OP(=O)([OH-])OC9C(OC(C9O)n1cnc2c1ccc(c2)OC)CO
CACTVS 3.385COc1ccc2n(cnc2c1)[C@H]3O[C@H](CO)[C@@H](O[P]([OH-])(=O)O[C@H](C)CNC(=O)CC[C@]4(C)[C@@H](CC(N)=O)C5=[N@+]6C4=C(C)C7=[N@+]8C(=CC9=[N@@+]%10C(=C(C)C%11=[N@+]([C@]5(C)[C@@](C)(CC(N)=O)[C@@H]%11CCC(N)=O)[Co]68%10)[C@@](C)(CC(N)=O)[C@@H]9CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O)[C@H]3O
CACTVS 3.385COc1ccc2n(cnc2c1)[CH]3O[CH](CO)[CH](O[P]([OH-])(=O)O[CH](C)CNC(=O)CC[C]4(C)[CH](CC(N)=O)C5=[N+]6C4=C(C)C7=[N+]8C(=CC9=[N+]%10C(=C(C)C%11=[N+]([C]5(C)[C](C)(CC(N)=O)[CH]%11CCC(N)=O)[Co]68%10)[C](C)(CC(N)=O)[CH]9CCC(N)=O)C(C)(C)[CH]7CCC(N)=O)[CH]3O
OpenEye OEToolkits 2.0.7CC1=C2[C@@]([C@@H](C3=[N+]2[Co]45[N+]6=C([C@H](C(C6=C3)(C)C)CCC(=O)N)C(=C7[N+]4=C([C@@H]([C@@]7(C)CCC(=O)NC[C@@H](C)OP(=O)([OH-])O[C@@H]8[C@H](O[C@@H]([C@@H]8O)n9cnc2c9ccc(c2)OC)CO)CC(=O)N)[C@@]2([N+]5=C1[C@H]([C@]2(C)CC(=O)N)CCC(=O)N)C)C)CCC(=O)N)(C)CC(=O)N
FormulaC61 H86 Co N13 O15 P
NameCO-5-METHOXYBENZIMIDAZOLYLCOBAMIDE;
FACTOR IIIM
ChEMBL
DrugBankDB02667
ZINC
PDB chain1y80 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1y80 Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica
Resolution1.7 Å
Binding residue
(original residue number in PDB)		D99 L100 H101 D102 I103 G104 V108 G144 M145 S146 L148 L149 T150 I175 G177 G178 A179 P196 D197 A198
Binding residue
(residue number reindexed from 1)		D15 L16 H17 D18 I19 G20 V24 G60 M61 S62 L64 L65 T66 I91 G93 G94 A95 P112 D113 A114
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D99 H101 T152
Catalytic site (residue number reindexed from 1) D15 H17 T68
Enzyme Commision number 2.1.1.13: methionine synthase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008705 methionine synthase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
Biological Process
GO:0009086 methionine biosynthetic process
GO:0015948 methanogenesis
GO:0032259 methylation
GO:0046653 tetrahydrofolate metabolic process
GO:0050667 homocysteine metabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Cellular Component
External links
PDB RCSB:1y80, PDBe:1y80, PDBj:1y80
PDBsum1y80
PubMed
UniProtQ2RJ67

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