SMTL ID : 8oru.1 (1 other biounit)

cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus bound to 2,3-diphosphoglycerate and ADP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 24 residues within 4Å: Chain A: K.144, R.145, I.146, G.147, K.148, T.149, A.150, M.302, E.304, M.307, V.333, F.334, R.335, T.351, T.352, A.353, P.354, V.357, L.361, E.403, K.405, N.428 Ligands: DG2.4, MG.6 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.145, A:R.145, A:I.146, A:G.147, A:K.148, A:T.149, A:A.150, A:E.304, A:E.304, A:F.334, A:R.335, A:T.351, A:T.352, A:T.352 Water bridges: A:K.405, A:K.405 Salt bridges: A:R.145, A:K.148, A:K.405 ADP.10: 26 residues within 4Å: Chain B: G.143, K.144, R.145, I.146, G.147, K.148, T.149, A.150, M.302, E.304, M.307, V.333, F.334, R.335, T.351, T.352, A.353, P.354, V.357, K.360, L.361, E.403, K.405, N.428 Ligands: MG.14, PO4.16 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.143, B:R.145, B:I.146, B:G.147, B:K.148, B:T.149, B:A.150, B:E.304, B:R.335, B:N.428 Water bridges: B:R.145, B:K.405, B:K.405 Salt bridges: B:R.145, B:R.145, B:K.148, B:K.405

6 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.5: 4 residues within 4Å: Chain A: Q.278, P.279, M.280, K.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.280, A:K.312 EDO.8: 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.11: 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 EDO.12: 3 residues within 4Å: Chain B: E.24, I.25, D.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.28 EDO.13: 3 residues within 4Å: Chain B: K.77, K.81, K.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.77, B:K.81

3 x DG2: (2R)-2,3-diphosphoglyceric acid(Non-covalent)

DG2.3: 3 residues within 4Å: Chain A: K.355, H.379, L.385 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:K.355, A:K.355, A:K.355, A:H.379, A:H.379 DG2.4: 13 residues within 4Å: Chain A: K.144, R.145, K.148, G.172, R.173, S.206, D.207, S.258, G.259, A.406 Chain B: E.44 Ligands: ADP.1, MG.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.145, A:R.173, A:S.258, A:G.259 Water bridges: A:K.405 Salt bridges: A:K.144, A:K.144, A:K.144, A:R.145, A:K.148, A:R.173, A:R.173 DG2.9: 5 residues within 4Å: Chain A: K.69 Chain B: K.355, H.379, L.385, R.388 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.355, B:K.355, B:K.355, B:H.379, B:H.379, B:R.388, A:K.69

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 6 residues within 4Å: Chain A: K.148, T.149, D.207, E.256 Ligands: ADP.1, DG2.4 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.14: 7 residues within 4Å: Chain B: R.145, K.148, T.149, D.207, E.256 Ligands: ADP.10, PO4.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.149, B:D.207, H2O.1, H2O.2 MG.15: 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.2

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 9 residues within 4Å: Chain B: K.144, R.145, K.148, R.173, D.207, S.258, G.259 Ligands: ADP.10, MG.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.207, B:G.259 Water bridges: B:R.145 Salt bridges: B:R.145, B:K.148, B:R.173

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
AAA

B
BBB

Cyclic 2,3-diphosphoglycerate synthetase

Related Entries With Identical Sequence