Structure of PDB 2i2x Chain L Binding Site BS01

Receptor Information

>2i2x Chain L (length=258) Species: 2208 (Methanosarcina barkeri)

MLDFTEASLKKVLTRYNVALEKALTPEEAAEELYPKDELIYPIAKAIFEG
EEDDVVEGLQAAIEAGKDPIDLIDDALMVGMGVVIRLYDEGVIFLPNVMM
SADAMLEGIEYCKENSGATPKTKGTVVCHVAEGDVHDIGKNIVTALLRAN
GYNVVDLGRDVPAEEVLAAVQKEKPIMLTGTALMTTTMYAFKEVNDMLLE
NGIKIPFACGGGAVNQDFVSQFALGVYGEEAADAPKIADAIIAGTTDVTE
LREKFHKH

Ligand information

• Ligand ID: B13
• InChI: InChI=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
• InChIKey: QJVWXASLTDBQFK-LAYHTZHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=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 3.341: C[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 3.341: C[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 1.5.0: CC1=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
• Formula: C60 H88 Co N13 O15 P
• Name: 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
• PDB chain: 2i2x Chain L Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2i2x Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): G133 D134 V135 H136 D137 I138 G139 V143 T179 T181 L183 M184 T185 A208 G210 G211 G212 G228 E229 E230 A231
• Binding residue (residue number reindexed from 1): G133 D134 V135 H136 D137 I138 G139 V143 T179 T181 L183 M184 T185 A208 G210 G211 G212 G228 E229 E230 A231
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): D134 H136 T187
• Catalytic site (residue number reindexed from 1): D134 H136 T187
• 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: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:0046653 tetrahydrofolate metabolic process
• GO:0050667 homocysteine metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:2i2x, PDBe:2i2x, PDBj:2i2x
• PDBsum: 2i2x
• PubMed: 17142327
• UniProt: Q46EH4|MTAC_METBF Methanol--corrinoid protein (Gene Name=mtaC)