SMTL ID : 6had.1

Human transketolase variant E160Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 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.5: 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:A.461, B:T.464

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: MG.3, TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.5 CA.6: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: MG.7, TPP.8 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.3: 8 residues within 4Å: Chain A: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: CA.2, TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.5 MG.7: 8 residues within 4Å: Chain B: D.155, G.156, N.185, L.187, G.188, K.244 Ligands: CA.6, TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.32

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 29 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, Q.160, N.185, L.187, G.188, Q.189, K.244, H.258, D.398 Chain B: G.340, D.341, T.342, I.364, E.366, T.388, F.392, R.395, Q.428 Ligands: CA.2, MG.3 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:F.392 Hydrogen bonds: B:Q.428, A:S.40, A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185 Water bridges: B:T.388, A:N.185, A:N.185 pi-Stacking: B:F.392 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 TPP.8: 29 residues within 4Å: Chain A: G.340, D.341, T.342, I.364, E.366, T.388, 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, Q.160, N.185, L.187, G.188, Q.189, K.244, H.258, D.398 Ligands: CA.6, MG.7 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:F.392 Hydrogen bonds: A:Q.428, B:S.40, B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185 Water bridges: A:T.388, B:N.185 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

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

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