Structure of PDB 1ccw Chain D Binding Site BS01

Receptor Information

>1ccw Chain D (length=483) Species: 1494 (Clostridium cochlearium)

MELKNKKWTDEEFHKQREEVLQQWPTGKEVDLQEAVDYLKKIPAEKNFAE
KLVLAKKKGITMAQPRAGVALLDEHIELLRYLQDEGGADFLPSTIDAYTR
QNRYDECENGIKESEKAGRSLLNGFPGVNFGVKGCRKVLEAVNLPLQARH
GTPDSRLLAEIIHAGGWTSNEGGGISYNVPYAKNVTIEKSLLDWQYCDRL
VGFYEEQGVHINREPFGPLTGTLVPPSMSNAVGITEALLAAEQGVKNITV
GYGECGNMIQDIAALRCLEEQTNEYLKAYGYNDVFVTTVFHQWMGGFPQD
ESKAFGVIVTATTIAALAGATKVIVKTPHEAIGIPTKEANAAGIKATKMA
LNMLEGQRMPMSKELETEMAVIKAETKCILDKMFELGKGDLAIGTVKAFE
TGVMDIPFGPSKYNAGKMMPVRDNLGCVRYLEFGNVPFTEEIKNYNRERL
QERAKFEGRDVSFQMVIDDIFAVGKGRLIGRPE

Ligand information

• Ligand ID: CNC
• InChI: InChI=1S/C62H90N13O14P.CN.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;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+3/p-1/t31-,34-,35-,36-,37+,41-,52-,53-,56?,57+,59-,60+,61+,62+;;/m1../s1
• InChIKey: SYZBZQWSWIJYAR-UVKKECPRSA-M
• SMILES:
  CACTVS 3.385: C[CH](CNC(=O)CC[C]1(C)[CH](CC(N)=O)[CH]2[N]([Co++]C#N)C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C]2(C)[C](C)(CC(N)=O)[CH]5CCC(N)=O)[C](C)(CC(N)=O)[CH]4CCC(N)=O)C(C)(C)[CH]3CCC(N)=O)O[P](O)(=O)O[CH]6[CH](O)[CH](O[CH]6CO)n7cnc8cc(C)c(C)cc78
  CACTVS 3.385: C[C@H](CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)[C@H]2[N@@]([Co++]C#N)C1=C(C)C3=NC(=CC4=NC(=C(C)C5=N[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]5CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)C(C)(C)[C@@H]3CCC(N)=O)O[P](O)(=O)O[C@H]6[C@@H](O)[C@H](O[C@@H]6CO)n7cnc8cc(C)c(C)cc78
  ACDLabs 12.01: NC(=O)CC1(C)C2=C(C)C=3C(CCC(N)=O)C(C)(CC(N)=O)C4(C)N=3[Co+2]35(C#N)N2=C(C=C2n3c(C(CCC(N)=O)C2(C)C)c(C)c2n5C4C(CC(N)=O)C2(C)CCC(=O)NCC(C)OP(=O)(O)OC2C(CO)OC(n3cnc4cc(C)c(C)cc43)C2O)C1CCC(N)=O
  OpenEye OEToolkits 2.0.7: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89(N5C4=C(C1=[N]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)C#N)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  OpenEye OEToolkits 2.0.7: 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[C@]6([C@@]([C@@H](C7=[N]6[Co+2]89(N5C4=C(C1=[N]8C(=CC2=[N]9C(=C7C)[C@@]([C@@H]2CCC(=O)N)(C)CC(=O)N)C([C@@H]1CCC(=O)N)(C)C)C)C#N)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
• Formula: C63 H89 Co N14 O14 P
• Name: CYANOCOBALAMIN
• PDB chain: 1ccw Chain C Residue 800

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ccw Glutamate mutase from Clostridium cochlearium: the structure of a coenzyme B12-dependent enzyme provides new mechanistic insights
• Resolution: 1.6 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 score: 1

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

External links

• PDB: RCSB:1ccw, PDBe:1ccw, PDBj:1ccw
• PDBsum: 1ccw
• PubMed: 10467146
• UniProt: P80077|GLME_CLOCO Glutamate mutase epsilon subunit (Gene Name=glmE)