Structure of PDB 4djf Chain E Binding Site BS02

Receptor Information
>4djf Chain E (length=441) Species: 1525 (Moorella thermoacetica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLTGLEIYKQLPKKNCGECGTPTCLAFAMNLASGKASLDSCPYVSDAARE
ALDAAAAPPIAKVVLGAGPTAVEMGDETELFRHDKRFYHETAIAIQVSDN
LSSEELKAKVEAINGLNFDRVGQHYTIQAIAIRHDADDPAAFKAAVASVA
AATQLNLVLMADDPDVLKEALAGVADRKPLLYAATGANYEAMTALAKENN
CPLAVYGNGLEELAELVDKIVALGHKQLVLDPGARETSRAIADFTQIRRL
AIKKRFRSFGYPIIALTTAANPLDEVLQAVNYVTKYASLVVLRTDAKEHL
LPLLSWRQNLYTDPQVPIRVEEKLNEIGAVNENSPVYVTTNFSLTYYSVE
GEIESTKIPSYLLSVDTDGLSVLTAYADGKFEAEKIAAVMKKVDLDNKVK
RHRIIIPGAVAVLKGKLEDLTGWEVIVGPREASGIVAFARA
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 chain4djf Chain E Residue 502 [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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PDB4djf Visualizing molecular juggling within a B12-dependent methyltransferase complex.
Resolution3.03 Å
Binding residue
(original residue number in PDB)		V339 T340 T346 V350 L371 S372 V373 L374 T375 A378 D379 P408 R431 A433
Binding residue
(residue number reindexed from 1)		V338 T339 T345 V349 L370 S371 V372 L373 T374 A377 D378 P407 R430 A432
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0015977 carbon fixation
GO:0044237 cellular metabolic process
GO:0046356 acetyl-CoA catabolic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4djf, PDBe:4djf, PDBj:4djf
PDBsum4djf
PubMed22419154
UniProtQ07340|ACSC_MOOTH Corrinoid/iron-sulfur protein large subunit (Gene Name=acsC)

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