SMTL ID : 8wa8.1

Human transketolase in complex with phosphite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.155, N.185, L.187 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.5 CA.9: 4 residues within 4Å: Chain B: D.155, N.185, L.187 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.22

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 25 residues within 4Å: Chain A: S.40, K.75, H.77, G.123, S.124, L.125, G.154, D.155, G.156, E.157, E.160, N.185, L.187, G.188, Q.189, K.244, H.258 Chain B: D.341, T.342, I.364, E.366, F.392, R.395, Q.428 Ligands: CA.1 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:F.392 Hydrogen bonds: B:Q.428, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185, A:L.187 Water bridges: B:T.388 pi-Stacking: B:F.392, A:H.77 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 TPP.10: 25 residues within 4Å: Chain A: D.341, T.342, I.364, E.366, F.392, R.395, Q.428 Chain B: S.40, K.75, H.77, G.123, S.124, L.125, G.154, D.155, G.156, E.157, E.160, N.185, L.187, G.188, Q.189, K.244, H.258 Ligands: CA.9 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185, B:L.187, A:Q.428 Water bridges: B:H.77 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258 pi-Stacking: B:H.77, A:F.392 Hydrophobic interactions: A:F.392

2 x PO3: PHOSPHITE ION(Non-covalent)

PO3.3: 4 residues within 4Å: Chain B: R.318, S.345, H.416, R.474 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:K.260, B:R.318, B:R.318, B:R.474 Salt bridges: B:R.318, B:H.416, B:R.474 PO3.11: 4 residues within 4Å: Chain A: R.318, S.345, H.416, R.474 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Water bridges: B:K.260, A:R.318, A:R.318, A:R.474 Salt bridges: A:R.318, A:H.416, A:R.474

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

EDO.4: 8 residues within 4Å: Chain A: P.63, N.68, D.69, R.70, F.71, W.86, D.119, R.379 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.63, A:N.68, A:F.71, A:F.71, A:R.379, A:R.379 EDO.5: 8 residues within 4Å: Chain A: L.158, S.159, W.164, R.205 Chain B: W.164, E.165, A.168, F.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.159, A:R.205 Water bridges: A:L.158, A:W.164 EDO.6: 2 residues within 4Å: Chain A: Q.10, A.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.10 Water bridges: A:K.283 EDO.7: 3 residues within 4Å: Chain A: Y.564, A.588, N.590 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.564 Water bridges: A:A.588, A:N.590, A:G.606 EDO.8: 6 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, F.117, T.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.73, A:V.120 Water bridges: A:F.117, A:D.119, A:D.119 EDO.12: 8 residues within 4Å: Chain B: P.63, N.68, D.69, R.70, F.71, W.86, D.119, R.379 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:P.63, B:N.68, B:F.71, B:F.71, B:R.379, B:R.379 Water bridges: B:D.119 EDO.13: 8 residues within 4Å: Chain A: W.164, E.165, A.168, F.209 Chain B: L.158, S.159, W.164, R.205 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.159, B:R.205 Water bridges: B:L.158, B:W.164 EDO.14: 2 residues within 4Å: Chain B: Q.10, A.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.10 Water bridges: B:K.283 EDO.15: 3 residues within 4Å: Chain B: Y.564, A.588, N.590 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.564, B:A.588, B:N.590, B:G.606 EDO.16: 6 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, F.117, T.118 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.73, B:V.120 Water bridges: B:F.117, B:D.119, B:D.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., Multifaceted Role of the Substrate Phosphate Group in Transketolase Catalysis. Acs Catalysis (2024)

Release Date

2024-01-24

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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