- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.23 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 7 residues within 4Å:- Chain A: M.6, L.26, L.29, I.32, M.89, Q.117
- Chain B: F.234
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.117
EDO.4: 3 residues within 4Å:- Chain A: P.279, M.280, K.312
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:M.280, A:K.312
EDO.5: 5 residues within 4Å:- Chain A: R.104, P.289, F.319, E.322, I.323
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.104, A:E.322
EDO.9: 8 residues within 4Å:- Chain A: F.234
- Chain B: M.6, L.26, L.29, I.32, I.87, M.89, Q.117
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.117
EDO.12: 4 residues within 4Å:- Chain B: Q.278, P.279, M.280, K.312
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:M.280, B:K.312
- 3 x DG2: (2R)-2,3-diphosphoglyceric acid(Non-covalent)
DG2.3: 14 residues within 4Å:- Chain A: K.144, R.145, K.148, T.149, G.172, R.173, S.206, D.207, S.258, G.259, A.406
- Chain B: K.45
- Ligands: ADP.1, MG.6
16 PLIP interactions:14 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.173, A:D.207, A:S.258, A:S.258, A:G.259, A:A.406
- Water bridges: A:R.145, A:R.145
- Salt bridges: A:K.144, A:R.145, A:R.145, A:K.148, A:R.173, A:R.173, B:K.45, B:K.45
DG2.10: 15 residues within 4Å:- Chain A: E.44, K.45
- Chain B: K.144, R.145, K.148, G.172, R.173, S.206, D.207, S.258, G.259, K.405, A.406
- Ligands: ADP.8, MG.13
13 PLIP interactions:11 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:R.173, B:D.207, B:G.259, B:A.406
- Water bridges: B:R.145, B:R.145
- Salt bridges: B:K.144, B:K.144, B:R.145, B:K.148, B:R.173, A:K.45, A:K.45
DG2.11: 4 residues within 4Å:- Chain A: K.69
- Chain B: K.355, H.379, L.385
6 PLIP interactions:4 interactions with chain B, 2 interactions with chain A- Salt bridges: B:K.355, B:K.355, B:K.355, B:H.379, A:K.69, A:K.69
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.6: 6 residues within 4Å:- Chain A: R.145, K.148, T.149, D.207
- Ligands: ADP.1, DG2.3
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.149, A:D.207, H2O.1, H2O.1
MG.7: 5 residues within 4Å:- Chain A: D.27, D.28, L.29, I.32, D.33
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.27, A:L.29, A:I.32, H2O.1, H2O.1
MG.13: 6 residues within 4Å:- Chain B: K.148, T.149, D.207, E.256
- Ligands: ADP.8, DG2.10
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.149, B:D.207, H2O.1, H2O.1
MG.14: 5 residues within 4Å:- Chain B: D.27, D.28, L.29, I.32, D.33
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.27, B:L.29, B:I.32, H2O.1
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- De Rose, S.A. et al., Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus . Front Microbiol (2023)
- Release Date
- 2023-12-06
- Peptides
- Cyclic 2,3-diphosphoglycerate synthetase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
DDD
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.23 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x DG2: (2R)-2,3-diphosphoglyceric acid(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- De Rose, S.A. et al., Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus . Front Microbiol (2023)
- Release Date
- 2023-12-06
- Peptides
- Cyclic 2,3-diphosphoglycerate synthetase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CCCB
DDD