Structure of PDB 7b2e Chain D Binding Site BS03

Receptor Information
>7b2e Chain D (length=548) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PELTDGFHLVIDALKLNGIETIYNVPGIPITDLGRLAQAEGLRVISFRHE
QNAGNAAAIAGFLTKKPGICLTVSAPGFLNGLTALANATTNCFPMILISG
SSEREIVDLQQGDYGEMDQLAIAKPLCKAAFRVLHAADIGIGVARAIRAA
VSGRPGGVYLDLPAKLFSQVIDADLGARSLVKVIDAAPAQLPAPAAIARA
LDVLKSAERPLIILGKGAAYAQADEAVRALVEESGIPYVPMSMAKGLLPD
THPLSAGAARSTALKDSDVVLLVGARLNWLLSHGKGKTWGEPGSKRFIQI
DIEPREMDSNVEIVAPVVGDIGSCVEALLDGIRKDWKGAPSNWLETLRGK
REANIAKMAPKLMKNSSPMCFHSALGALRTVIKERPDAILVNEGCNTLDL
ARGIIDMYQPRKRLDVGTWGVMGIGMGFAVAAAVETGKPVLAVEGDSAFG
FSGMEVETICRYELPVCIVIFNNNGIFRGTDTDPTGRDPGTTVFVKNSRY
DKMMEAFGGVGVNVTTPDELKRAVDEAMNSGKPTLINAEIDPAAGSEG
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 chain7b2e 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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PDB7b2e Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		C112 R174 K236 G237 M261 G294 R296 D321 I322 D340 I341
Binding residue
(residue number reindexed from 1)		C92 R154 K216 G217 M241 G274 R276 D301 I302 D320 I321
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) V45 G47 I48 P49 I50 E70 V93 Y134 G135 A184 L301 G414 G440 M442 I496 R498 G499 T502
Catalytic site (residue number reindexed from 1) V25 G27 I28 P29 I30 E50 V73 Y114 G115 A164 L281 G394 G420 M422 I476 R478 G479 T482
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:7b2e, PDBe:7b2e, PDBj:7b2e
PDBsum7b2e
PubMed34484855
UniProtC5AX46

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