SMTL ID : 4kxy.1

Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihydroxyethyl)-3-deaza-ThDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.423, K.597 Chain B: A.33, R.101, K.102 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: R.21, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Y.564, A.588, N.590 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Q.189, S.256, W.257, H.258 Chain B: N.344 Ligand excluded by PLIP EDO.6: 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.10: 8 residues within 4Å: Chain A: E.165, A.168, F.169, C.362, A.365, N.368 Chain B: S.159 Ligands: EDO.26 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: Q.10, K.11 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Y.137, Y.141, Y.173 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: L.158, S.159, W.164 Chain B: W.164, E.165, A.168, F.209 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.475, N.477, V.510, E.514, P.598, L.602 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Q.127, A.131, S.371, V.374, Q.399 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: D.333, R.358, T.382 Ligand excluded by PLIP EDO.19: 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.20: 4 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: P.63, N.68, D.69, R.70, F.71, W.86, D.119, R.379 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: N.344 Chain B: Q.189, S.256, W.257, H.258 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: W.164, E.165, A.168, F.209 Chain B: L.158, S.159, W.164 Ligands: EDO.10, EDO.27 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: F.209 Chain B: L.158, W.164, L.195, Y.202, R.205 Ligands: EDO.26 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: Q.10, K.11, A.14 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: A.33, R.101, K.102 Chain B: E.423, K.597 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.33: 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.34: 5 residues within 4Å: Chain B: Q.127, A.131, S.371, V.374, Q.399 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: Y.137, Y.141, Y.173 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: D.155, N.185, L.187 Ligands: 1U0.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.19 CA.25: 4 residues within 4Å: Chain B: D.155, N.185, L.187 Ligands: 1U0.24 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.30

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

NA.8: 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.32: 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:N.411, B:T.464

2 x 1U0: 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate(Non-covalent)

1U0.9: 26 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, I.364, E.366, F.392, R.395, Q.428 Ligands: CA.7 25 PLIP interactions: 20 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.125, A:Q.189, B:F.392, B:F.392 Hydrogen bonds: A:H.37, A:S.40, A:H.77, A:G.123, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185, A:H.258, B:Q.428 Water bridges: A:H.77, B:T.388 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244 pi-Stacking: A:H.77, B:F.392 1U0.24: 26 residues within 4Å: Chain A: D.341, 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.25 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.125, A:F.392, A:F.392 Hydrogen bonds: B:H.37, B:S.40, B:G.123, B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185, A:Q.428 Water bridges: B:H.77, A:T.388 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244 pi-Stacking: B:H.77, A:F.392

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

SO4.16: 4 residues within 4Å: Chain A: R.318, S.345, H.416, R.474 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.345 Water bridges: A:R.318, A:R.318, A:H.416, A:R.474, A:R.474, A:R.474, B:Q.189, B:K.260, B:K.260, B:K.260, B:K.260 Salt bridges: A:R.318, A:H.416, A:R.474 SO4.31: 4 residues within 4Å: Chain B: R.318, S.345, H.416, R.474 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.345 Water bridges: B:R.318, B:R.318, B:R.474, B:R.474, A:Q.189, A:G.259, A:K.260, A:K.260, A:K.260 Salt bridges: B:R.318, B:H.416, B:R.474

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
B

Transketolase

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