SMTL ID : 6rjb.1

Human transketolase variant T382E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 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: MG.2, CA.3 22 PLIP interactions: 17 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.40, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:E.160, A:N.185, B:Q.428 Water bridges: A:N.185, 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 pi-Stacking: A:H.77, B:F.392 Hydrophobic interactions: B:D.341, B:F.392 TPP.28: 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: MG.29, CA.30 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.40, 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.110, A:T.388 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258 Hydrophobic interactions: A:F.392 pi-Stacking: A:F.392

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: TPP.1, CA.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.7 MG.29: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: TPP.28, CA.30 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.30

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: TPP.1, MG.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.7 CA.30: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: TPP.28, MG.29 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.30

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.420, P.475, N.477, V.510, E.514, P.598, A.599, L.602, R.609 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.477, A:N.477 Water bridges: A:E.476, A:E.476, A:E.476, A:E.514, A:R.609 GOL.31: 7 residues within 4Å: Chain A: K.260 Chain B: R.318, N.344, S.345, F.389, H.416, R.474 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.318, B:R.318, B:N.344, B:S.345, B:H.416, B:R.474, B:R.474 Water bridges: A:K.260, A:K.260

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

EDO.5: 11 residues within 4Å: Chain A: F.52, Y.58, P.63, N.68, D.69, R.70, F.71, W.86, F.117, R.379 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 13 residues within 4Å: Chain A: F.52, F.71, V.72, L.73, L.82, W.86, P.111, F.117, T.118, D.119, V.120, T.122 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 10 residues within 4Å: Chain A: L.158, S.159, W.164, P.194, L.195, Y.202, R.205 Chain B: F.209 Ligands: EDO.11, PEG.52 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Y.564, L.587, A.588, V.589, N.590, G.606 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Q.189, S.190, S.256, W.257, H.258, K.260 Chain B: N.344 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: Y.563, Y.564, E.565, V.589, N.590, R.591 Chain B: P.441, T.442, K.538 Ligand excluded by PLIP EDO.11: 13 residues within 4Å: Chain A: L.158, S.159, E.160, G.161, W.164, R.205 Chain B: W.164, E.165, A.168, F.209, A.365 Ligands: EDO.7, PEG.52 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: R.21, L.22, S.25, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.13: 10 residues within 4Å: Chain A: V.120, A.121, Q.127, A.131, S.371, V.374, Q.399, M.402, A.403, S.406 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain A: E.423, G.596, K.597, E.600 Chain B: A.33, S.35, L.100, R.101, K.102, I.103 Ligand excluded by PLIP EDO.15: 9 residues within 4Å: Chain A: L.92, E.96, D.106, L.107, K.114, Q.115, A.116, F.117 Ligands: EDO.19 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.137, Y.141, Y.173, D.357 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: A.326, K.327, H.330, E.354 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: P.307, S.308, Y.309, Q.323, K.327, E.455 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: F.91, L.92, A.93 Ligands: EDO.15 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: M.199, I.215, V.216, D.217, K.241 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: D.217, G.218, H.219, K.241, T.242, F.243, R.246 Ligands: EDO.20 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: R.246, G.247, E.252 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: N.409, A.462, N.463, T.464, K.465 Ligands: NA.25 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: R.318, N.344, S.345, F.389, H.416, R.474 Chain B: Q.189 Ligand excluded by PLIP EDO.32: 10 residues within 4Å: Chain A: F.209 Chain B: L.158, S.159, W.164, P.194, L.195, Y.202, R.205 Ligands: PEG.27, EDO.35 Ligand excluded by PLIP EDO.33: 13 residues within 4Å: Chain B: F.52, F.71, V.72, L.73, L.82, W.86, P.111, F.117, T.118, D.119, V.120, T.122 Ligands: EDO.38 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain A: P.441, K.538 Chain B: Y.563, Y.564, E.565, V.589, N.590, R.591 Ligand excluded by PLIP EDO.35: 13 residues within 4Å: Chain A: W.164, E.165, A.168, F.209, A.365 Chain B: L.158, S.159, E.160, G.161, W.164, R.205 Ligands: PEG.27, EDO.32 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain A: N.344 Chain B: Q.189, S.190, S.256, W.257, H.258, K.260 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain A: A.33, S.35, L.100, R.101, K.102, I.103 Chain B: E.423, G.596, K.597 Ligand excluded by PLIP EDO.38: 11 residues within 4Å: Chain B: F.52, Y.58, P.63, N.68, D.69, R.70, F.71, W.86, F.117, R.379 Ligands: EDO.33 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590, F.605, G.606 Ligands: EDO.42 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain B: L.92, E.96, D.106, L.107, K.114, Q.115, A.116, F.117 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain B: S.420, P.475, N.477, V.510, E.514, P.598, A.599, L.602 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain B: N.590, R.591 Ligands: EDO.39 Ligand excluded by PLIP EDO.43: 9 residues within 4Å: Chain B: R.21, L.22, S.25, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain B: Q.10, K.11, A.14, I.284, L.285 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain B: M.199, I.215, V.216, D.217, E.223, K.241 Ligands: EDO.49 Ligand excluded by PLIP EDO.46: 12 residues within 4Å: Chain B: I.315, A.316, T.317, S.449, D.450, S.473, P.475, E.476, N.477, G.509, V.510, H.513 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain B: I.27, Q.28, T.31, K.264, A.267, E.268, I.271 Ligand excluded by PLIP EDO.48: 8 residues within 4Å: Chain A: L.195, I.201, R.205 Chain B: A.168, S.171, I.172, F.209, G.210 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain B: D.217, G.218, H.219, K.241, T.242, F.243, R.246 Ligands: EDO.45 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: N.300, I.301, R.302, E.459, L.460, N.463 Ligand excluded by PLIP EDO.51: 10 residues within 4Å: Chain B: V.120, A.121, Q.127, A.131, S.371, V.374, Q.399, M.402, A.403, S.406 Ligand excluded by PLIP

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

NA.25: 6 residues within 4Å: Chain A: N.411, A.461, A.462, T.464, C.468 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.411, A:T.464, A:T.464 NA.26: 9 residues within 4Å: Chain A: S.74, T.122, G.123, S.124, L.125, G.126, Q.127, G.128, E.157 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.74, A:S.124, A:G.126, A:Q.127, A:G.128 Water bridges: A:G.76, A:S.124

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

PEG.27: 15 residues within 4Å: Chain A: E.165, A.166, A.168, F.169, I.172, Y.173, C.362, Y.363, A.365, N.368 Chain B: S.159, P.194, R.205 Ligands: EDO.32, EDO.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.159 Water bridges: B:R.205 PEG.52: 14 residues within 4Å: Chain A: S.159, P.194, R.205 Chain B: E.165, A.166, A.168, F.169, I.172, C.362, Y.363, A.365, N.368 Ligands: EDO.7, EDO.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, S. et al., Low-barrier hydrogen bonds in enzyme cooperativity. Nature (2019)

Release Date

2019-09-11

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase