Structure of PDB 2ji8 Chain B Binding Site BS04

Receptor Information
>2ji8 Chain B (length=556) Species: 847 (Oxalobacter formigenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHE
QHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSG
SSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTA
VSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARA
ADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPD
NHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQID
IQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVD
GNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDN
TRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFG
FSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYD
MMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVESGRI
KSLNVV
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 chain2ji8 Chain B Residue 1565 [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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PDB2ji8 Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
Resolution2.15 Å
Binding residue
(original residue number in PDB)		C98 R160 G221 K222 G223 M247 G280 A281 R282 D306 I307 D325 I326
Binding residue
(residue number reindexed from 1)		C92 R154 G215 K216 G217 M241 G274 A275 R276 D300 I301 D319 I320
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) V31 G33 I34 P35 I36 E56 V79 Y120 E121 E122 A170 M287 G400 G426 M428 D452 N479 G481 I482 K484 G485 A488 P547
Catalytic site (residue number reindexed from 1) V25 G27 I28 P29 I30 E50 V73 Y114 E115 E116 A164 M281 G394 G420 M422 D446 N473 G475 I476 K478 G479 A482 P541
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:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0042802 identical protein binding
GO:0043531 ADP 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:2ji8, PDBe:2ji8, PDBj:2ji8
PDBsum2ji8
PubMed17637344
UniProtP40149|OXC_OXAFO Oxalyl-CoA decarboxylase (Gene Name=oxc)

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