Structure of PDB 1gyl Chain A Binding Site BS01

Receptor Information

>1gyl Chain A (length=352) Species: 3562 (Spinacia oleracea)

MEITNVNEYEAIAKQKLPKMVYDFYASGAEDQWTLAENRNAFSRILFRPR
ILIDVTNIDMTTTILGFKISMPIMIAPTAMQKMAHPEGEYATARAASAAG
TIMTLSSWATSSVEEVASTGPGIRFFQLYVYKDRNVVAQLVRRAERAGFK
AIALTVDTPRLGRREADIKNRFVLPPFLTLKNFEGIDLGKGLSSYVAGQI
DRSLSWKDVAWLQTITSLPILVKGVITAEDARLAVQHGAAGIIVSNHGAR
QLDYVPATIMALEEVVKAAQGRIPVFLDGGVRRGTDVFKALALGAAGVFI
GRPVVFSLAAEGEAGVKKVLQMMRDEFELTMALSGCRSLKEISRSHIAAD
WD

Ligand information

• Ligand ID: FMN
• InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 1gyl Chain A Residue 370

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1gyl Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): F24 A76 P77 A79 S106 Q127 Y129 T155 K230 H254 R257 D285 G286 R289 G308 R309
• Binding residue (residue number reindexed from 1): F24 A76 P77 A79 S106 Q127 Y129 T155 K223 H247 R250 D278 G279 R282 G301 R302
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S106 Y129 T155 D157 K230 H254
• Catalytic site (residue number reindexed from 1): S106 Y129 T155 D157 K223 H247
• Enzyme Commision number: 1.1.3.15: (S)-2-hydroxy-acid oxidase.

Gene Ontology

Molecular Function

• GO:0003973 (S)-2-hydroxy-acid oxidase activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity

Biological Process

• GO:0009853 photorespiration
• GO:0009854 oxidative photosynthetic carbon pathway
• GO:0051707 response to other organism

Cellular Component

• GO:0005777 peroxisome

External links

• PDB: RCSB:1gyl, PDBe:1gyl, PDBj:1gyl
• PDBsum: 1gyl
• PubMed: 7705356
• UniProt: P05414|GOX_SPIOL Glycolate oxidase