Structure of PDB 3w8d Chain A Binding Site BS02

Receptor Information

>3w8d Chain A (length=260) Species: 511 (Alcaligenes faecalis)

MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLE
SKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIE
EFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASV
NKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAI
SQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTT
LSLDGGWTAR

Ligand information

• Ligand ID: DXX
• InChI: InChI=1S/C4H6O4/c1-2(3(5)6)4(7)8/h2H,1H3,(H,5,6)(H,7,8)
• InChIKey: ZIYVHBGGAOATLY-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: CC(C(O)=O)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(C(=O)O)C(=O)O
  ACDLabs 10.04: O=C(O)C(C(=O)O)C
• Formula: C4 H6 O4
• Name: METHYLMALONIC ACID
• ChEMBL: CHEMBL1232416
• DrugBank: DB04183
• ZINC: ZINC000000901289
• PDB chain: 3w8d Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3w8d X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and methylmalonate
• Resolution: 1.37 Å
• Binding residue (original residue number in PDB): Q94 S142 H144 K152 Y155 W187 Q196 W257
• Binding residue (residue number reindexed from 1): Q94 S142 H144 K152 Y155 W187 Q196 W257
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G15 N114 S142 Y155 K159 I200
• Catalytic site (residue number reindexed from 1): G15 N114 S142 Y155 K159 I200
• Enzyme Commision number: 1.1.1.30: 3-hydroxybutyrate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003858 3-hydroxybutyrate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:3w8d, PDBe:3w8d, PDBj:3w8d
• PDBsum: 3w8d
• UniProt: D0VWQ0