Structure of PDB 7ayg Chain D Binding Site BS01

Receptor Information
>7ayg Chain D (length=546) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELTDGFHLVIDALKLNGIETIYNVPGIPITDLGRLAQAEGLRVISFRHEQ
NAGNAAAIAGFLTKKPGICLTVSAPGFLNGLTALANATTNCFPMILISGS
SEREIVDLQQGDYEEMDQLAIAKPLCKAAFRVLHAADIGIGVARAIRAAV
SGRPGGVYLDLPAKLFSQVIDADLGARSLVKVIDAAPAQLPAPAAIARAL
DVLKSAERPLIILGKGAAYAQADEAVRALVEESGIPYVPMSMAKGLLPDT
HPLSAGAARSTALKDSDVVLLVGARLNWLLSHGKGKTWGEPGSKRFIQID
IEPREMDSNVEIVAPVVGDIGSCVEALLDGIRKDWKGAPSNWLETLRGKR
EANIAKMAPKLMKNSSPMCFHSALGALRTVIKERPDAILVNEGANTLDLA
RGIIDMYQPRKRLDVGTWGVMGIGMGFAVAAAVETGKPVLAVEGDSAFGF
SGMEVETICRYELPVCIVIFNNNGIYRGTDTDPTGRDPGTTVFVKNSRYD
KMMEAFGGVGVNVTTPDELKRAVDEAMNSGKPTLINAEIDPAAGSE
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain7ayg Chain D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ayg Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F391 A415 N416 T417 M442 G465 D466 S467 A468 F471 N493 G495 I496 Y497
Binding residue
(residue number reindexed from 1)		F370 A394 N395 T396 M421 G444 D445 S446 A447 F450 N472 G474 I475 Y476
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V45 G47 I48 P49 I50 E70 V93 Y134 E135 A184 L301 G414 G440 M442 I496 R498 G499 T502
Catalytic site (residue number reindexed from 1) V24 G26 I27 P28 I29 E49 V72 Y113 E114 A163 L280 G393 G419 M421 I475 R477 G478 T481
Enzyme Commision number 4.1.1.8: oxalyl-CoA decarboxylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008949 oxalyl-CoA decarboxylase activity
GO:0016829 lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0001561 fatty acid alpha-oxidation
GO:0019752 carboxylic acid metabolic process
GO:0033611 oxalate catabolic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7ayg, PDBe:7ayg, PDBj:7ayg
PDBsum7ayg
PubMed34484855
UniProtC5AX46

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