SMTL ID : 4kxx.1

Human transketolase in covalent complex with donor ketose D-sedoheptulose-7-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

2 x 1Y7: (2R,3R,4S,5R,6S)-2,3,4,5,6,7-hexahydroxyheptyl dihydrogen phosphate(Non-covalent)

1Y7.1: 15 residues within 4Å: Chain A: H.37, H.77, H.110, G.123, Q.189, H.258, G.259 Chain B: R.318, S.345, F.389, H.416, D.424, Q.428, R.474 Ligands: TPP.2 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:H.110, B:D.424, B:Q.428 Water bridges: A:H.77, A:R.101, A:H.258, A:K.260, A:K.260, A:K.260, B:R.318, B:R.318, B:N.344, B:N.344, B:R.474 Salt bridges: B:R.318, B:H.416, B:R.474 1Y7.17: 15 residues within 4Å: Chain A: R.318, S.345, F.389, H.416, D.424, Q.428, R.474 Chain B: H.37, H.77, H.110, G.123, Q.189, H.258, G.259 Ligands: TPP.18 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:D.424, A:Q.428, B:H.77, B:H.110 Water bridges: A:R.318, A:R.318, A:N.344, A:N.344, A:R.474, B:H.77, B:R.101, B:H.258, B:K.260, B:K.260, B:K.260 Salt bridges: A:R.318, A:H.416, A:R.474

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 26 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: 1Y7.1, MG.13 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185, B:Q.428 Water bridges: A:N.185, B:T.388 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 Hydrophobic interactions: B:F.392 pi-Stacking: B:F.392 TPP.18: 26 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: 1Y7.17, MG.29 16 PLIP interactions: 3 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:F.392 Hydrogen bonds: A:Q.428, B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185 pi-Stacking: A:F.392 Water bridges: B:N.185 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258

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

EDO.3: 7 residues within 4Å: Chain A: Q.127, A.131, S.371, V.374, Q.399, M.402, A.403 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: L.158, S.159, W.164 Chain B: W.164, E.165, A.168, F.209 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: N.590, R.591 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: R.21, S.25, A.84, A.87, E.88, E.94, L.97 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Q.189, S.256, W.257, H.258 Chain B: N.344 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: L.158, S.159, W.164, L.195, Y.202, R.205 Chain B: F.209 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.12: 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.14: 6 residues within 4Å: Chain A: E.423, G.596, K.597 Chain B: A.33, R.101, K.102 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Y.563, Y.564, E.565, V.589, N.590 Chain B: K.538 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: Q.127, A.131, S.371, V.374, Q.399, M.402, A.403 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: W.164, E.165, A.168, F.209 Chain B: L.158, S.159, W.164 Ligands: EDO.25 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: N.590, R.591 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: R.21, S.25, A.84, A.87, E.88, E.94, L.97 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: N.344 Chain B: Q.189, S.256, W.257, H.258 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain A: F.209 Chain B: L.158, S.159, W.164, L.195, Y.202, R.205 Ligands: EDO.21 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.28: 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.30: 6 residues within 4Å: Chain A: A.33, R.101, K.102 Chain B: E.423, G.596, K.597 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: K.538 Chain B: Y.563, Y.564, E.565, V.589, N.590 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 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.18 MG.29: 4 residues within 4Å: Chain B: D.155, N.185, L.187 Ligands: TPP.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.48

2 x NA: SODIUM ION(Non-functional Binders)

NA.15: 4 residues within 4Å: Chain A: N.411, A.461, T.464, C.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.411, A:T.464, A:T.464 NA.31: 4 residues within 4Å: Chain B: N.411, A.461, T.464, C.468 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.411, B:A.461, B:T.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ludtke, S. et al., Sub-angstrom-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate. Nat Chem (2013)

Release Date

2013-08-21

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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