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

Crystal structure of transketolase from Geobacillus stearothermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 14 residues within 4Å: Chain A: E.180, F.426, D.453, Y.454, L.455, R.456, P.457 Chain B: E.175, G.176, V.177, F.426, D.453, Y.454, P.457 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.175 Hydrogen bonds: A:E.180 EDO.2: 6 residues within 4Å: Chain A: R.371, S.397, S.398, F.448, H.475, R.534 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.371, A:R.371, A:H.475, A:R.534 EDO.3: 6 residues within 4Å: Chain A: S.199, D.201, L.208, R.229, E.257, K.259 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.199, A:D.201, A:R.229, A:R.229, A:E.257, A:E.257, A:K.259 Water bridges: A:Y.197 EDO.4: 6 residues within 4Å: Chain A: G.349, K.442, P.468, S.523, T.524 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.442 EDO.5: 8 residues within 4Å: Chain A: P.67, N.68, R.72, Y.118, T.121, P.122, G.123, V.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.123 Water bridges: A:V.124 EDO.6: 4 residues within 4Å: Chain A: K.36, A.37, Q.104, Q.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.36 Water bridges: A:Q.107 EDO.7: 10 residues within 4Å: Chain A: R.345, A.346, G.349, K.350, L.351, Q.387, G.440, L.441, K.442 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.346, A:A.346, A:Q.387, A:G.440 EDO.14: 7 residues within 4Å: Chain B: G.349, L.441, K.442, P.468, S.523, T.524 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.349 EDO.15: 10 residues within 4Å: Chain B: R.345, A.346, G.349, K.350, L.351, Q.387, G.440, L.441, K.442 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.349, B:K.350, B:G.440 EDO.16: 8 residues within 4Å: Chain B: A.479, Q.535, D.536, V.537, P.538, S.575, M.629, M.661 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.535

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 5 residues within 4Å: Chain A: A.396, S.397, L.402, W.420 Chain B: D.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.397

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.9: 26 residues within 4Å: Chain A: M.44, H.81, G.129, P.130, L.131, G.169, D.170, G.171, D.172, E.175, N.200, I.202, S.203, L.204, I.262, H.276 Chain B: A.393, D.394, L.395, V.423, E.425, F.448, F.451, Y.454, H.487 Ligands: MG.10 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:D.394, B:F.451, B:Y.454 Hydrogen bonds: B:H.487, A:G.129, A:L.131, A:D.170, A:G.171, A:E.175, A:N.200, A:I.202, A:L.204 Water bridges: B:E.425, A:M.44, A:H.81 pi-Stacking: B:F.451 Salt bridges: A:H.81, A:H.81, A:H.276 TPP.17: 26 residues within 4Å: Chain A: A.393, D.394, L.395, V.423, E.425, F.448, F.451, Y.454, H.487 Chain B: M.44, H.81, G.129, P.130, L.131, G.169, D.170, G.171, D.172, E.175, N.200, I.202, S.203, L.204, I.262, H.276 Ligands: MG.18 22 PLIP interactions: 5 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:D.394, A:V.423, A:Y.454, B:L.131, B:L.131 Hydrogen bonds: A:H.487, B:G.129, B:L.131, B:D.170, B:G.171, B:N.200, B:L.204 pi-Stacking: A:F.451 Water bridges: B:M.44, B:H.81, B:H.81, B:D.170, B:D.198, B:D.198 Salt bridges: B:H.81, B:H.81, B:H.276

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: D.170, N.200, I.202, S.203 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.170, A:I.202, H2O.1 MG.18: 5 residues within 4Å: Chain B: D.170, N.200, I.202, S.203 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.170, B:I.202, H2O.7

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: H.336, P.337, E.338, L.339 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: Y.118, G.119 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: N.68, F.70, R.72, R.74, H.438 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: R.371, S.398, H.475, R.534 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leogrande, C. et al., Crystal structure of transketolase from Geobacillus stearothermophilus. To Be Published

Release Date

2023-03-01

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase

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