Structure of PDB 7ayg Chain D Binding Site BS02

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 IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7ayg Chain D Residue 602 [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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PDB7ayg Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		C112 R174 G235 K236 G237 M261 G294 A295 R296 D321 I322 D340 I341
Binding residue
(residue number reindexed from 1)		C91 R153 G214 K215 G216 M240 G273 A274 R275 D300 I301 D319 I320
Annotation score2
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

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

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