Structure of PDB 2ldb Chain B Binding Site BS04

Receptor Information

>2ldb Chain B (length=301) Species: 1422 (Geobacillus stearothermophilus)

MKNNGGARVVVIGAGFVGASYVFALMNQGIADEIVLIDANESKAIGDAMD
FNHGKVFAPKPVDIWDYDDCRDADLVVICAGALDLVDKNIAIFRSIVESV
MASGFQGLFLVATNPVDILTYATWKFSGLPHERVIGSGTILDTARFRFLL
GEYFSVAPQNVHAYIIGEHGDTELPVWSQAYIGVMPIRKLVESKDLERIF
VNVRDAAYQIIEKKGATYYGIAMGLARVTRAILHNENAILTVSAYLDGLY
GERDVYIGVPAVINRNGIREVIEIELNDDEKNRFHHSAATLKSVLARAFT
R

Ligand information

• Ligand ID: FBP
• InChI: InChI=1S/C6H14O12P2/c7-4-3(1-16-19(10,11)12)18-6(9,5(4)8)2-17-20(13,14)15/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4-,5+,6-/m1/s1
• InChIKey: RNBGYGVWRKECFJ-ARQDHWQXSA-N
• SMILES:
  CACTVS 3.341: O[C@H]1[C@H](O)[C@@](O)(CO[P](O)(O)=O)O[C@@H]1CO[P](O)(O)=O
  CACTVS 3.341: O[CH]1[CH](O)[C](O)(CO[P](O)(O)=O)O[CH]1CO[P](O)(O)=O
  ACDLabs 10.04: O=P(O)(O)OCC1OC(O)(COP(=O)(O)O)C(O)C1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O
• Formula: C6 H14 O12 P2
• Name: 1,6-di-O-phosphono-beta-D-fructofuranose;
  BETA-FRUCTOSE-1,6-DIPHOSPHATE;
  FRUCTOSE-1,6-BISPHOSPHATE;
  1,6-di-O-phosphono-beta-D-fructose;
  1,6-di-O-phosphono-D-fructose;
  1,6-di-O-phosphono-fructose
• ChEMBL: CHEMBL97893
• DrugBank: DB04551
• ZINC: ZINC000004096694
• PDB chain: 2ldb Chain C Residue 6

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ldb Structure determination and refinement of Bacillus stearothermophilus lactate dehydrogenase.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): Q183 H186
• Binding residue (residue number reindexed from 1): Q159 H162
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D166 R169 H193
• Catalytic site (residue number reindexed from 1): D142 R145 H169
• Enzyme Commision number: 1.1.1.27: L-lactate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004459 L-lactate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

Biological Process

• GO:0006089 lactate metabolic process
• GO:0006090 pyruvate metabolic process
• GO:0006096 glycolytic process
• GO:0019752 carboxylic acid metabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2ldb, PDBe:2ldb, PDBj:2ldb
• PDBsum: 2ldb
• PubMed: 2330370
• UniProt: P00344|LDH_GEOSE L-lactate dehydrogenase (Gene Name=ldh)