Structure of PDB 2ji8 Chain B Binding Site BS05

Receptor Information

>2ji8 Chain B (length=556) Species: 847 (Oxalobacter formigenes)

VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHE
QHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSG
SSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTA
VSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARA
ADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPD
NHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQID
IQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVD
GNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDN
TRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFG
FSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYD
MMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVESGRI
KSLNVV

Ligand information

• Ligand ID: FYN
• InChI: InChI=1S/C22H36N7O17P3S/c1-22(2,17(33)20(34)25-4-3-13(31)24-5-6-50-11-30)8-43-49(40,41)46-48(38,39)42-7-12-16(45-47(35,36)37)15(32)21(44-12)29-10-28-14-18(23)26-9-27-19(14)29/h9-12,15-17,21,32-33H,3-8H2,1-2H3,(H,24,31)(H,25,34)(H,38,39)(H,40,41)(H2,23,26,27)(H2,35,36,37)/t12-,15-,16-,17+,21-/m1/s1
• InChIKey: SXMOKYXNAPLNCW-GORZOVPNSA-N
• SMILES:
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC=O
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC=O)O
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC=O)O
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC=O
  ACDLabs 10.04: O=CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
• Formula: C22 H36 N7 O17 P3 S
• ZINC: ZINC000008551237
• PDB chain: 2ji8 Chain B Residue 1566

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ji8 Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): A263 A264 T265 R266 A267 L286 N358 L362 G400 L404 R408 M409 S553 R555 I556
• Binding residue (residue number reindexed from 1): A257 A258 T259 R260 A261 L280 N352 L356 G394 L398 R402 M403 S547 R549 I550
• Annotation score: 4

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

External links

• PDB: RCSB:2ji8, PDBe:2ji8, PDBj:2ji8
• PDBsum: 2ji8
• PubMed: 17637344
• UniProt: P40149|OXC_OXAFO Oxalyl-CoA decarboxylase (Gene Name=oxc)