SMTL ID : 6ha3.1

Human transketolase variant E160Q in covalent complex with donor ketose D-fructose-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-dimer

Ligands

2 x T6F: 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-6-O-phosphono-D-glucitol(Non-covalent)

T6F.1: 36 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, Q.160, N.185, L.187, G.188, Q.189, K.244, H.258 Chain B: R.318, D.341, T.342, S.345, I.364, E.366, F.389, F.392, R.395, H.416, D.424, Q.428, R.474 Ligands: EDO.2, CA.15, MG.16, EDO.30 28 PLIP interactions: 9 interactions with chain B, 19 interactions with chain A Hydrophobic interactions: B:F.392, A:L.125 Hydrogen bonds: B:S.345, B:Q.428, A:S.40, A:H.110, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185, A:Q.189, A:Q.189, A:H.258 Water bridges: B:N.344, B:T.388, A:H.77 Salt bridges: B:R.318, B:H.416, B:R.474, A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 pi-Stacking: B:F.392 T6F.17: 36 residues within 4Å: Chain A: R.318, D.341, T.342, S.345, I.364, E.366, F.389, F.392, R.395, H.416, D.424, Q.428, R.474 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, Q.160, N.185, L.187, G.188, Q.189, K.244, H.258 Ligands: EDO.14, EDO.18, CA.31, MG.32 28 PLIP interactions: 19 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.125, A:F.392 Hydrogen bonds: B:S.40, B:H.110, B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185, B:Q.189, B:Q.189, B:H.258, A:S.345, A:Q.428 Water bridges: B:H.77, A:N.344, A:T.388 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258, A:R.318, A:H.416, A:R.474 pi-Stacking: A:F.392

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

EDO.2: 10 residues within 4Å: Chain A: S.35, G.36, H.37, R.101, G.259, K.260, P.261 Chain B: D.424, R.474 Ligands: T6F.1 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, P.111, F.117, T.118 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Y.564, L.587, A.588, N.590, F.605, G.606 Ligands: EDO.9 Ligand excluded by PLIP EDO.5: 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.6: 11 residues within 4Å: Chain A: F.52, M.56, Y.58, P.63, N.68, D.69, R.70, F.71, W.86, F.117, R.379 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: L.92, E.96, D.106, L.107, K.114, Q.115, A.116, F.117 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: N.590, R.591 Ligands: EDO.4 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: D.62, R.64, N.65, P.66 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain A: S.420, P.475, E.476, N.477, V.510, H.513, E.514, P.598, A.599, L.602 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: D.155, G.156, L.158, S.159, A.193, P.194, L.195, Y.202 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 9 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.12 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.318, N.344, S.345, R.474 Chain B: K.260 Ligands: T6F.17 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: D.424, R.474 Chain B: S.35, G.36, H.37, R.101, G.259, K.260, P.261 Ligands: T6F.17 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, P.111, F.117, T.118 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590, F.605, G.606 Ligands: EDO.25 Ligand excluded by PLIP EDO.21: 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.22: 11 residues within 4Å: Chain B: F.52, M.56, Y.58, P.63, N.68, D.69, R.70, F.71, W.86, F.117, R.379 Ligand excluded by PLIP EDO.23: 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.25: 3 residues within 4Å: Chain B: N.590, R.591 Ligands: EDO.20 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: D.62, R.64, N.65, P.66 Ligand excluded by PLIP EDO.27: 10 residues within 4Å: Chain B: S.420, P.475, E.476, N.477, V.510, H.513, E.514, P.598, A.599, L.602 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain B: D.155, G.156, L.158, S.159, A.193, P.194, L.195, Y.202 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain A: F.209 Chain B: L.158, S.159, W.164, P.194, L.195, Y.202, R.205 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: K.260 Chain B: R.318, N.344, S.345, R.474 Ligands: T6F.1 Ligand excluded by PLIP

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

NA.8: 5 residues within 4Å: Chain A: N.411, A.461, A.462, T.464, C.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.411, A:N.411, A:T.464 NA.24: 5 residues within 4Å: Chain B: N.411, A.461, A.462, T.464, C.468 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.411, B:T.464, B:T.464

2 x CA: CALCIUM ION(Non-covalent)

CA.15: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: T6F.1, MG.16 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.7 CA.31: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: T6F.17, MG.32 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.32

2 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: T6F.1, CA.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.7 MG.32: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: T6F.17, CA.31 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.32

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

2019-08-21

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

Related Entries With Identical Sequence