SMTL ID : 8waa.1

Human transketolase soaked with donor ketose D-xylulose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: THD.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.3 CA.15: 4 residues within 4Å: Chain B: D.155, N.185, L.187 Ligands: THD.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.30

2 x 3GR: D-Glyceraldehyde(Non-covalent)

3GR.2: 5 residues within 4Å: Chain A: R.318, N.344, S.345, H.416, R.474 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.318, A:R.318, A:N.344, A:H.416, A:R.474 Water bridges: B:K.260, B:K.260 3GR.16: 4 residues within 4Å: Chain B: R.318, S.345, H.416, R.474 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.318, B:R.318, B:N.344, B:R.474 Water bridges: B:H.416, B:D.424, A:K.260, A:K.260

2 x THD: 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

THD.3: 27 residues within 4Å: Chain A: H.37, S.40, K.75, H.77, H.110, 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 19 PLIP interactions: 3 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:F.392, A:L.125 Hydrogen bonds: B:Q.428, A:H.110, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185 pi-Stacking: B:F.392 Water bridges: A:H.77, A:N.185 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 THD.17: 27 residues within 4Å: Chain A: D.341, T.342, I.364, E.366, F.392, R.395, Q.428 Chain B: H.37, S.40, K.75, H.77, H.110, 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.15 20 PLIP interactions: 5 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:T.342, A:F.392 Hydrogen bonds: A:Q.428, B:H.110, B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185, B:N.185 Water bridges: A:T.388, B:H.77 pi-Stacking: A:F.392 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258

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

EDO.4: 5 residues within 4Å: Chain A: E.423, K.597 Chain B: A.33, R.101, K.102 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: P.63, N.68, D.69, R.70, F.71, W.86, R.379 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.21, S.25, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: L.158, S.159, W.164 Chain B: W.164, E.165, A.168, F.209 Ligands: EDO.12 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: Y.563, Y.564, E.565, V.589, N.590 Chain B: P.441, K.538 Ligand excluded by PLIP EDO.12: 8 residues within 4Å: Chain A: L.158, S.159, W.164, L.195, Y.202, R.205 Chain B: F.209 Ligands: EDO.9 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: Q.189, S.256, W.257, H.258 Chain B: N.344 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: S.171, I.172 Chain B: P.194, L.195 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: A.33, R.101, K.102 Chain B: E.423, K.597 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: E.165, A.168, F.169, I.172, C.362, Y.363, A.365 Chain B: S.159 Ligands: EDO.24 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: P.63, N.68, D.69, R.70, F.71, W.86, R.379 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: R.21, S.25, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: F.209 Chain B: L.158, W.164, L.195, Y.202, R.205 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain A: W.164, E.165, A.168, F.209 Chain B: L.158, S.159, W.164 Ligands: EDO.19, EDO.23 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: Q.127, G.128, A.131, S.371, V.374, Q.399 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: N.344 Chain B: Q.189, S.256, W.257, H.258 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: P.441, K.538 Chain B: Y.563, Y.564, E.565, V.589, N.590 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: N.590, R.591 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: P.475, N.477, V.510, E.514, P.598, L.602 Ligand excluded by PLIP

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
B

Transketolase

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