Structure of PDB 6a0y Chain A Binding Site BS01

Receptor Information

>6a0y Chain A (length=334) Species: 31958 (Amycolatopsis orientalis)

TYVSLADLERAARDVLPGEIFDFLAGGSGTEASLVANRTALERVFVIPRM
LRDLTDVTTEIDIFGRRAALPMAVAPVAYQRLFHPEGELAVARAARDAGV
PYTICTLSSVSLEEIAAVGGRPWFQLFWLRDEKRSLDLVRRAEDAGCEAI
VFTVDVPWMGRRLRDMRNGFALPEWVTAANFDFAPATWESVEAVRAHTDL
PVVLKGILAVEDARRAVDAGAGGIVVSNHGGRQLDGAVPGIEMLGEIVAA
VSGGCEVLVDGGIRSGGDVLKATALGASAVLVGRPVMWALAAAGQDGVRQ
LLELLAEEVRDAMGLAGCESVGAARRLNTKLGVV

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: 6a0y Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6a0y Biochemical and structural explorations of alpha-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): P77 V78 A79 Q126 F128 T154 K228 H252 G253 R255 D283 G285 R287 G306 R307
• Binding residue (residue number reindexed from 1): P76 V77 A78 Q125 F127 T153 K205 H229 G230 R232 D260 G262 R264 G283 R284
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F128 D156 H252
• Catalytic site (residue number reindexed from 1): F127 D155 H229
• Enzyme Commision number: 1.1.3.46: 4-hydroxymandelate oxidase.

Gene Ontology

Molecular Function

• GO:0004459 L-lactate dehydrogenase activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0016899 oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor

Biological Process

• GO:0017000 antibiotic biosynthetic process
• GO:0033072 vancomycin biosynthetic process

External links

• PDB: RCSB:6a0y, PDBe:6a0y, PDBj:6a0y
• PDBsum: 6a0y
• PubMed: 31373572
• UniProt: O52792|HMO_AMYOR 4-hydroxymandelate oxidase (Gene Name=hmo)