Structure of PDB 3giy Chain A Binding Site BS01

Receptor Information

>3giy Chain A (length=353) Species: 303 (Pseudomonas putida)

NLFNVEDYRKLAQKRLPKMVYDYLEGGAEDEYGVKHNRDVFQQWRFKPKR
LVDVSRRSLQAEVLGKRQSMPLLIGPTALNGALWPKGDLALARAATKAGI
PFVLSTASNMSIEDLARQCDGDLWFQLYVIHREIAQGMVLKALHTGYTTL
VLTTDVAVNGYRERDLHNRFKIPPFLTLKNFEGIDLGKMDKANLEMQAAL
MSRQMDASFNWEALRWLRDLWPHKLLVKGLLSAEDADRCIAEGADGVILS
NHGGRQLDCAISPMEVLAQSVAKTGKPVLIDSGFRRGSDIVKALALGAEA
VLLGRATLYGLAARGETGVDEVLTLLKADIDRTLAQIGCPDITSLSPDYL
QNE

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: 3giy Chain A Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3giy Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Y26 P79 T80 A81 S108 Q129 Y131 T156 K231 H255 G256 R258 D284 S285 G286 R288 G307 R308
• Binding residue (residue number reindexed from 1): Y23 P76 T77 A78 S105 Q126 Y128 T153 K228 H252 G253 R255 D281 S282 G283 R285 G304 R305
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S108 Y131 T156 D158 K231 H255
• Catalytic site (residue number reindexed from 1): S105 Y128 T153 D155 K228 H252
• Enzyme Commision number: 1.1.99.31: (S)-mandelate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004459 L-lactate dehydrogenase activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0033720 (S)-mandelate dehydrogenase activity

Biological Process

• GO:0009056 catabolic process
• GO:0018924 mandelate metabolic process
• GO:0019596 mandelate catabolic process

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:3giy, PDBe:3giy, PDBj:3giy
• PDBsum: 3giy
• PubMed: 19465768
• UniProt: P20932|MDLB_PSEPU (S)-mandelate dehydrogenase (Gene Name=mdlB)