Structure of PDB 8oru Chain AAA Binding Site BS02

Receptor Information

>8oru Chain AAA (length=459) Species: 523846 (Methanothermus fervidus DSM 2088)

GETKKMICLVDGEHYFPVVKDSIEILDDLEHIDVVAVVFIGGTEKLQIED
PKEYSEKLGKPVFFGPDPKKIPYDVIKKCVKKYNADIVMDLSDEPVVDYT
KRFRIASIVLKEGAVYQGADFKFEPLTEYDVLEKPSIKIIGTGKRIGKTA
VSAYAARVIHKHKYNPCVVAMGRGGPREPEIVEGNKIEITAEYLLEQADK
GVHAASDHWEDALMSRILTVGCRRCGGGMLGDTFITNVKRGAEIANKLDS
DFVIMEGSGAAIPPVKTNRQIVTVGANQPMININNFFGPFRIGLADLVII
TMCEEPMATTEKIKKVEKFIKEINPSANVIPTVFRPKPVGNVEGKKVLFA
TTAPKVVVGKLVNYLESKYGCDVVGVTPHLSNRPLLRRDLKKYINKADLM
LTELKAAAVDVATRVAIEAGLDVVYCDNIPVVIDESYGNIDDAIIEVVEM
AIDDFKNNR

Ligand information

• Ligand ID: DG2
• InChI: InChI=1S/C3H8O10P2/c4-3(5)2(13-15(9,10)11)1-12-14(6,7)8/h2H,1H2,(H,4,5)(H2,6,7,8)(H2,9,10,11)/t2-/m1/s1
• InChIKey: XOHUEYCVLUUEJJ-UWTATZPHSA-N
• SMILES:
  CACTVS 3.385: OC(=O)[C@@H](CO[P](O)(O)=O)O[P](O)(O)=O
  OpenEye OEToolkits 2.0.5: C(C(C(=O)O)OP(=O)(O)O)OP(=O)(O)O
  CACTVS 3.385: OC(=O)[CH](CO[P](O)(O)=O)O[P](O)(O)=O
  OpenEye OEToolkits 2.0.5: C([C@H](C(=O)O)OP(=O)(O)O)OP(=O)(O)O
• Formula: C3 H8 O10 P2
• Name: (2R)-2,3-diphosphoglyceric acid;
  2,3-Bisphosphoglyceric acid;
  2,3-bisphosphoglycerate;
  2,3-BPG;
  2,3-diphosphoglyceric acid;
  2,3-diphosphoglycerate;
  2,3-DPG;
  (2~{R})-2,3-diphosphonooxypropanoic acid
• ZINC: ZINC000003869234
• PDB chain: 8oru Chain AAA Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8oru Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus
• Resolution: 2.23 Å
• Binding residue (original residue number in PDB): K356 H380
• Binding residue (residue number reindexed from 1): K355 H379
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 6.5.1.9: cyclic 2,3-diphosphoglycerate synthase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0036356 cyclic 2,3-diphosphoglycerate synthetase activity

Biological Process

• GO:0006094 gluconeogenesis
• GO:1901369 cyclic 2,3-bisphospho-D-glycerate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:8oru, PDBe:8oru, PDBj:8oru
• PDBsum: 8oru
• PubMed: 38045033
• UniProt: O93732|CPGS_METFV Cyclic 2,3-diphosphoglycerate synthetase (Gene Name=cpgS)