Structure of PDB 3kb6 Chain A Binding Site BS01

Receptor Information

>3kb6 Chain A (length=333) Species: 63363 (Aquifex aeolicus)

NVLFTSVPQEDVPFYQEALKDLSLKIYTTDVSKVPENELKKAELISVFVY
DKLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESV
AEHTFAMILTLVKRLKRIEDRVKKLNFSQDSEILARELNRLTLGVIGTGR
IGSRVAMYGLAFGMKVLCYDVVKREDLKEKGCVYTSLDELLKESDVISLH
VPYTKETHHMINEERISLMKDGVYLINTARGKVVDTDALYRAYQRGKFSG
LGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITPHIAYYTDK
SLERIREETVKVVKAFVKGDLEQIKGNFVVGPS

Ligand information

• Ligand ID: LAC
• InChI: InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)/t2-/m1/s1
• InChIKey: JVTAAEKCZFNVCJ-UWTATZPHSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C(O)C
  CACTVS 3.341: C[CH](O)C(O)=O
  OpenEye OEToolkits 1.5.0: C[C@H](C(=O)O)O
  CACTVS 3.341: C[C@@H](O)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(C(=O)O)O
• Formula: C3 H6 O3
• Name: LACTIC ACID
• ChEMBL: CHEMBL358850
• DrugBank: DB03066
• ZINC: ZINC000004658562
• PDB chain: 3kb6 Chain A Residue 399

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kb6 Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).
• Resolution: 2.12 Å
• Binding residue (original residue number in PDB): F49 S72 V73 G74 Y96 R231 H294
• Binding residue (residue number reindexed from 1): F48 S71 V72 G73 Y95 R230 H293
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): S97 R231 D255 E260 H294
• Catalytic site (residue number reindexed from 1): S96 R230 D254 E259 H293
• Enzyme Commision number: 1.1.1.28: D-lactate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008720 D-lactate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

External links

• PDB: RCSB:3kb6, PDBe:3kb6, PDBj:3kb6
• PDBsum: 3kb6
• PubMed: 20054113
• UniProt: O66939