SMTL ID : 3m49.1

Crystal Structure of Transketolase Complexed with Thiamine Diphosphate from Bacillus anthracis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 22 residues within 4Å: Chain A: M.55, H.92, G.140, P.141, L.142, G.180, D.181, G.182, E.186, N.211, I.213, L.215, I.273, H.287 Chain B: D.405, V.434, E.436, F.462, Y.465, H.498 Ligands: MG.16, GOL.19 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.142, A:L.215, A:L.215, B:D.405, B:V.434, B:F.462, B:Y.465 Hydrogen bonds: A:G.140, A:L.142, A:D.181, A:G.182, A:N.211, A:I.213 Water bridges: A:D.183 Salt bridges: A:H.92, A:H.92, A:H.287, A:H.287 pi-Stacking: B:F.462 TPP.25: 23 residues within 4Å: Chain A: D.405, L.406, V.434, E.436, F.462, Y.465, H.498 Chain B: M.55, H.92, G.140, P.141, L.142, G.180, D.181, G.182, E.186, N.211, I.213, S.214, L.215, I.273, H.287 Ligands: SO4.2 22 PLIP interactions: 7 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:D.405, A:L.406, A:V.434, A:F.462, A:Y.465, B:L.142, B:L.215 Water bridges: A:E.436, B:G.180, B:G.180, B:N.211, B:I.213 pi-Stacking: A:F.462 Hydrogen bonds: B:G.140, B:L.142, B:D.181, B:G.182, B:E.186, B:N.211 Salt bridges: B:H.92, B:H.92, B:H.287

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: H.498 Chain B: H.52, H.92, H.126, G.140, H.287 Ligands: TPP.25 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Water bridges: A:D.494, B:H.92, B:H.92 Salt bridges: A:H.498, B:H.52, B:H.92, B:H.126 Hydrogen bonds: B:G.140 SO4.6: 4 residues within 4Å: Chain A: R.382, S.409, H.486, R.545 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.409 Water bridges: A:R.382, A:R.382 Salt bridges: A:R.382, A:H.486, A:R.545 SO4.7: 1 residues within 4Å: Chain A: R.615 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.537, A:K.537, A:K.537, A:K.537 Salt bridges: A:K.537, A:R.615 SO4.8: 1 residues within 4Å: Chain A: R.263 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.263, A:R.263, A:R.263 Salt bridges: A:R.263 SO4.9: 6 residues within 4Å: Chain A: S.26, Q.31, N.35, A.302, Y.303 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.26, A:Q.31, A:N.35, A:N.35 Water bridges: A:R.38 SO4.22: 4 residues within 4Å: Chain A: P.511, N.512, V.513, D.614 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.512, A:V.513 Water bridges: A:A.509 SO4.26: 5 residues within 4Å: Chain B: P.511, N.512, V.513, K.537, D.614 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.512, B:V.513, B:V.513 Water bridges: B:K.537, B:K.537, A:D.660 Salt bridges: B:K.537 SO4.32: 4 residues within 4Å: Chain B: R.382, S.409, H.486, R.545 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.409 Water bridges: B:R.382, B:H.486, B:D.494 Salt bridges: B:R.382, B:H.486, B:R.545 SO4.38: 1 residues within 4Å: Chain B: R.615 5 PLIP interactions: 5 interactions with chain B Water bridges: B:T.535, B:N.536, B:R.615, B:R.615 Salt bridges: B:R.615

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 2 residues within 4Å: Chain A: W.119, G.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.120 FMT.10: 2 residues within 4Å: Chain A: Y.559, E.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.559 Water bridges: A:Y.559 FMT.15: 5 residues within 4Å: Chain A: V.568, S.606, S.626, V.627, P.629 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.606 Water bridges: A:E.575, A:E.575 FMT.18: 3 residues within 4Å: Chain A: H.27, I.29, E.316 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.27 FMT.21: 7 residues within 4Å: Chain A: G.58, G.244, N.245, T.271, T.272, F.275 Ligands: PEG.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.245, A:T.272, A:T.272, A:T.272 FMT.23: 2 residues within 4Å: Chain A: R.529, Y.559 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.529 Water bridges: A:Y.559 FMT.28: 4 residues within 4Å: Chain A: S.50, R.117 Chain B: E.493, R.545 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.493, B:R.545, B:R.545, A:R.117 Water bridges: B:E.493, B:E.493, A:N.49 FMT.30: 2 residues within 4Å: Chain B: E.674, Y.675 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.661 FMT.31: 3 residues within 4Å: Chain B: Y.559, E.560, A.563 No protein-ligand interaction detected (PLIP) FMT.33: 4 residues within 4Å: Chain B: H.102, T.109, M.110 Ligands: GOL.34 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.109, B:D.111 FMT.35: 5 residues within 4Å: Chain B: T.79, F.81, R.83, H.449, G.450 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.83, B:R.83, B:R.85 FMT.37: 4 residues within 4Å: Chain B: A.304, W.305, T.306, A.307 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.306, B:A.307

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.26, Q.31, L.32, N.35, Y.303, A.304, W.305 Ligands: SO4.9, GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.35 Water bridges: A:S.26 GOL.5: 4 residues within 4Å: Chain A: N.369, P.371, A.391, E.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.394 GOL.19: 7 residues within 4Å: Chain A: H.52, L.215, H.287 Chain B: F.459, D.494, H.498 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.494, B:H.498, A:H.287 GOL.20: 6 residues within 4Å: Chain A: L.32, A.304, W.305, T.306, A.307 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.304, A:W.305, A:T.306, A:A.307 GOL.24: 3 residues within 4Å: Chain A: K.47, K.114, Q.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.47, A:K.47, A:K.114 Water bridges: A:Q.118, A:Q.118 GOL.29: 2 residues within 4Å: Chain B: R.529, Y.559 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.529, B:R.529 Water bridges: B:T.558, B:T.558 GOL.34: 3 residues within 4Å: Chain B: E.315, Y.318 Ligands: FMT.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.315 GOL.36: 4 residues within 4Å: Chain A: D.216 Chain B: A.407, G.408, Y.413 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.221, B:G.408, B:G.408, B:Y.413 Hydrogen bonds: B:A.407

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.11: 2 residues within 4Å: Chain A: R.684, K.685 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.684, A:R.684 Salt bridges: A:R.684, A:K.685

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.12: 6 residues within 4Å: Chain A: Y.129, G.130, H.131, T.132, M.476 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.130

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 8 residues within 4Å: Chain A: Y.129, A.447, M.476, Q.477, L.478, P.479, T.535 Ligands: PG5.12 No protein-ligand interaction detected (PLIP) PEG.17: 8 residues within 4Å: Chain A: E.242, D.243, G.244, N.245, R.270, T.271, T.272 Ligands: FMT.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.245, A:T.272 Water bridges: A:R.270, A:R.270

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 3 residues within 4Å: Chain A: E.315, Y.318, R.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.315, A:R.322 Water bridges: A:Y.318

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 4 residues within 4Å: Chain A: D.181, N.211, I.213 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, A:I.213, H2O.14

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.27: 6 residues within 4Å: Chain B: N.369, L.370, P.371, A.387, A.391, E.394 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.394 Water bridges: B:A.391, B:A.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Transketolase Complexed with Thiamine Diphosphate from Bacillus anthracis. To be Published

Release Date

2010-04-07

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase

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