Structure of PDB 4jgi Chain B Binding Site BS01

Receptor Information
>4jgi Chain B (length=206) Species: 49338 (Desulfitobacterium hafniense) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIDLNASAQAMSDLDEGAINEVVDKVMAKADADAAQELIKAFQQGMTKVG
ERFDSGEYFIGDLIFAGEILQAAMDKLKPALEKRAKIVLATVEGDLHDIG
KNIFRTMAEASGFEVFDLGIDVPVKIIVDKVKEVNPEIVGLSGVLTLALD
SMRETVDALKAEGLRNDLKVIIGGVPVNENVCQRVGADDFSTNAADGVKI
CQRWVG
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 chain4jgi Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jgi Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		L63 D100 L101 H102 D103 I104 G105 F109 G145 S147 L150 G178 G179 V180 S196 T197 N198 A199
Binding residue
(residue number reindexed from 1)		L63 D95 L96 H97 D98 I99 G100 F104 G140 S142 L145 G173 G174 V175 S191 T192 N193 A194
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D100 H102 A153
Catalytic site (residue number reindexed from 1) D95 H97 A148
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008705 methionine synthase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
Biological Process
GO:0009086 methionine biosynthetic process
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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Biological Process
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Cellular Component
External links
PDB RCSB:4jgi, PDBe:4jgi, PDBj:4jgi
PDBsum4jgi
PubMed23897483
UniProtQ8RPG0

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