SMTL ID : 8qmf.1

Transketolase from Vibrio vulnificus in complex with thiamin pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 residues within 4Å: Chain A: A.28, H.65, G.113, P.114, L.115, G.153, D.154, G.155, E.159, N.184, I.186, S.187, I.188, I.245, H.259 Chain B: D.379, L.380, V.408, E.410, F.433, F.436, Y.439, H.472 Ligands: EDO.6, MG.8 18 PLIP interactions: 4 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.380, B:F.436, B:Y.439, A:L.115, A:I.188, A:I.188 pi-Stacking: B:F.436, A:H.65 Hydrogen bonds: A:G.113, A:L.115, A:D.154, A:G.155, A:N.184 Water bridges: A:A.28, A:N.63 Salt bridges: A:H.65, A:H.65, A:H.259 TPP.11: 24 residues within 4Å: Chain A: D.379, L.380, V.408, E.410, F.436, Y.439, H.472 Chain B: A.28, H.65, G.113, P.114, L.115, G.153, D.154, G.155, E.159, N.184, I.186, S.187, I.188, I.245, H.259 Ligands: EDO.16, MG.17 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.115, B:I.188, B:I.188, A:L.380, A:V.408, A:F.436, A:Y.439 Hydrogen bonds: B:G.113, B:L.115, B:D.154, B:G.155, B:N.184, B:I.186 Water bridges: B:A.28 Salt bridges: B:H.65, B:H.65, B:H.259 pi-Stacking: B:H.65, A:F.436

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

EDO.2: 7 residues within 4Å: Chain A: W.40, H.46, D.57, F.59, Y.79, G.107, E.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.107, A:E.109 Water bridges: A:N.47 EDO.3: 5 residues within 4Å: Chain A: W.181, V.192, F.196, D.198, T.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.200 Water bridges: A:T.200 EDO.4: 4 residues within 4Å: Chain A: D.189, G.190, H.191, W.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.191, A:H.191 EDO.5: 4 residues within 4Å: Chain A: S.558, E.559, F.644, F.649 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.559 EDO.6: 7 residues within 4Å: Chain A: H.25, I.188, H.259 Chain B: F.433, D.468, H.472 Ligands: TPP.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.468, A:H.259 EDO.7: 7 residues within 4Å: Chain A: I.614, D.616, T.632 Chain B: R.482, L.483, T.484, P.485 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:N.486, A:D.616, A:D.616 Hydrogen bonds: A:D.616 EDO.10: 6 residues within 4Å: Chain A: R.482, L.483, T.484, P.485 Chain B: I.614, D.616 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.484, B:D.616, B:D.616 Water bridges: A:M.487, A:D.589 EDO.12: 8 residues within 4Å: Chain B: W.40, L.44, H.46, D.57, F.59, Y.79, G.107, E.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.79, B:G.107, B:E.109 EDO.13: 6 residues within 4Å: Chain B: W.181, D.183, V.192, F.196, D.198, T.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.198 Water bridges: B:T.200 EDO.14: 3 residues within 4Å: Chain B: D.189, G.190, H.191 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:H.405 Hydrogen bonds: B:H.191, B:H.191 EDO.15: 5 residues within 4Å: Chain B: S.558, E.559, L.562, F.644, F.649 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.559, B:E.559 EDO.16: 7 residues within 4Å: Chain A: F.433, D.468, H.472 Chain B: H.25, I.188, H.259 Ligands: TPP.11 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.468 Water bridges: B:H.259

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: D.154, N.184, I.186 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.154, A:I.186, H2O.3 MG.17: 4 residues within 4Å: Chain B: D.154, N.184, I.186 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.154, B:I.186, H2O.16

1 x NI: NICKEL (II) ION(Non-covalent)

NI.9: 3 residues within 4Å: Chain A: E.672, H.675, H.677 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.672, A:H.675, A:H.677

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Georges, R.N. et al., Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior. Protein Sci. (2024)

Release Date

2024-02-07

Peptides

Transketolase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 2