Structure of PDB 2i2x Chain M Binding Site BS03

Receptor Information
>2i2x Chain M (length=459) Species: 2208 (Methanosarcina barkeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKRYTSMAYANADEMTFGVSKYPVKAGLDLEIGAGYTIPEINYAPRPEAG
ASKEKLIKEYERITTDVMERMVQVGFPAIILETEHVQQMSNNPSWGAEVA
HAQKTIMEKYHDEYGIKCALRHTIGDIRENREFLQLRGDKYSVFLEAFEQ
CAENGADLLSVESMGGKEVFDYAVLRNDIPGLLYSIGCLGSIDMELIWTD
ISKIAKKTGTISAGDTDCAQANTAMFIGGGLLNKNLAHTIAVIARAISAP
RSLVAYEAGAVGPGKDCGYENIIVKAITGMPMTMEGKTSTCAHSDVMGNL
VMQCCDCWSNESVEYHGEFGGTTVQCWSETLAYDCALMNTALETKNDKVL
RDLMMLSDRYRDPQAYMLAYDNAYRVGQSIVKDGDNIYLRAKNAAIECCN
IIEEGAAGKLELSRFETKALADAKAALEALPDDMDKFMDDCLTKYKSEVK
VFKPENYGF
Ligand information
Ligand IDB13
InChIInChI=1S/C60H88N13O15P.Co/c1-28(87-89(84,85)88-51-39(26-74)86-55(50(51)83)73-27-68-37-20-31(75)10-14-38(37)73)25-67-47(82)18-19-57(6)35(21-44(64)79)54-60(9)59(8,24-46(66)81)34(13-17-43(63)78)49(72-60)30(3)53-58(7,23-45(65)80)32(11-15-41(61)76)36(69-53)22-40-56(4,5)33(12-16-42(62)77)48(70-40)29(2)52(57)71-54;/h10,14,20,22,27-28,32-35,39-40,49-52,54-55,74-75,83H,11-13,15-19,21,23-26H2,1-9H3,(H2,61,76)(H2,62,77)(H2,63,78)(H2,64,79)(H2,65,80)(H2,66,81)(H,67,82)(H,84,85);/q-4;+4/b36-22-,48-29-,53-30-;/t28-,32-,33-,34-,35+,39-,40+,49-,50-,51-,52+,54-,55+,57-,58+,59+,60+;/m1./s1
InChIKeyQJVWXASLTDBQFK-LAYHTZHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C2C(C(C3=CC4C(C(C5=C(C6C(C(C7N6[Co](N45)(N32)N8C1C(C(C78C)(C)CC(=O)N)CCC(=O)N)CC(=O)N)(C)CCC(=O)NCC(C)OP(=O)(O)OC9C(OC(C9O)n1cnc2c1ccc(c2)O)CO)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N
CACTVS 3.341C[CH](CNC(=O)CC[C]1(C)[CH](CC(N)=O)[CH]2N3[CH]1C(=C4[CH](CCC(N)=O)C(C)(C)[CH]5C=C6[CH](CCC(N)=O)[C](C)(CC(N)=O)C7=C(C)[CH]8[CH](CCC(N)=O)[C](C)(CC(N)=O)[C]2(C)N8[Co]3(N45)N67)C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(O)ccc%10%11
CACTVS 3.341C[C@H](CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)[C@H]2N3[C@H]1C(=C4[C@@H](CCC(N)=O)C(C)(C)[C@@H]5C=C6[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)C7=C(C)[C@@H]8[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@@]2(C)N8[Co@@]3(N45)N67)C)O[P@](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(O)ccc%10%11
OpenEye OEToolkits 1.5.0CC1=C2[C@@]([C@@H](C3=CC4C([C@@H](C5=C(C6[C@]([C@H]([C@H]7N6[Co](N45)(N32)N8C1[C@H]([C@]([C@]78C)(C)CC(=O)N)CCC(=O)N)CC(=O)N)(C)CCC(=O)NC[C@@H](C)O[P@@](=O)(O)O[C@@H]9[C@H](O[C@@H]([C@@H]9O)n1cnc2c1ccc(c2)O)CO)C)CCC(=O)N)(C)C)CCC(=O)N)(C)CC(=O)N
FormulaC60 H88 Co N13 O15 P
Name5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
ChEMBL
DrugBank
ZINC
PDB chain2i2x Chain N Residue 500 [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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PDB2i2x Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K169 A221 F228 A294 S314
Binding residue
(residue number reindexed from 1)		K167 A219 F226 A292 S312
Annotation score2
Enzymatic activity
Enzyme Commision number 2.1.1.90: methanol--corrinoid protein Co-methyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0046872 metal ion binding
GO:0047152 methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase activity
Biological Process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2i2x, PDBe:2i2x, PDBj:2i2x
PDBsum2i2x
PubMed17142327
UniProtQ46EH3|MTAB_METBF Methanol--corrinoid protein co-methyltransferase (Gene Name=mtaB)

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