Structure of PDB 1cb7 Chain D Binding Site BS01

Receptor Information
>1cb7 Chain D (length=483) Species: 1494 (Clostridium cochlearium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELKNKKWTDEEFHKQREEVLQQWPTGKEVDLQEAVDYLKKIPAEKNFAE
KLVLAKKKGITMAQPRAGVALLDEHIELLRYLQDEGGADFLPSTIDAYTR
QNRYDECENGIKESEKAGRSLLNGFPGVNFGVKGCRKVLEAVNLPLQARH
GTPDSRLLAEIIHAGGWTSNEGGGISYNVPYAKNVTIEKSLLDWQYCDRL
VGFYEEQGVHINREPFGPLTGTLVPPSMSNAVGITEALLAAEQGVKNITV
GYGECGNMIQDIAALRCLEEQTNEYLKAYGYNDVFVTTVFHQWMGGFPQD
ESKAFGVIVTATTIAALAGATKVIVKTPHEAIGIPTKEANAAGIKATKMA
LNMLEGQRMPMSKELETEMAVIKAETKCILDKMFELGKGDLAIGTVKAFE
TGVMDIPFGPSKYNAGKMMPVRDNLGCVRYLEFGNVPFTEEIKNYNRERL
QERAKFEGRDVSFQMVIDDIFAVGKGRLIGRPE
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 chain1cb7 Chain C Residue 800 [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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PDB1cb7 Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R100 Y181 T220 M294 G295 G296 F297 E330 G333 I334 F471
Binding residue
(residue number reindexed from 1)		R100 Y181 T220 M294 G295 G296 F297 E330 G333 I334 F471
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R100 E171
Catalytic site (residue number reindexed from 1) R100 E171
Enzyme Commision number 5.4.99.1: methylaspartate mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0031419 cobalamin binding
GO:0050097 methylaspartate mutase activity
Biological Process
GO:0019553 glutamate catabolic process via L-citramalate
GO:0019670 anaerobic glutamate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1cb7, PDBe:1cb7, PDBj:1cb7
PDBsum1cb7
PubMed10467146
UniProtP80077|GLME_CLOCO Glutamate mutase epsilon subunit (Gene Name=glmE)

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