SMTL ID : 6tth.1

PKM2 in complex with L-threonine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Non-covalent)

FBP.1: 17 residues within 4Å: Chain A: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, W.532, R.533, P.534, G.535, S.536, G.537, F.538, T.539 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.449, A:K.450, A:S.451, A:R.453, A:S.454, A:G.531, A:R.533, A:G.535, A:S.536, A:G.537, A:F.538 Water bridges: A:R.472, A:R.472 Salt bridges: A:K.450, A:R.506 FBP.3: 17 residues within 4Å: Chain B: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, W.532, R.533, P.534, G.535, S.536, G.537, F.538, T.539 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.449, B:K.450, B:S.451, B:R.453, B:S.454, B:G.531, B:R.533, B:G.535, B:S.536, B:G.537, B:F.538 Water bridges: B:R.472, B:R.472 Salt bridges: B:K.450, B:R.506 FBP.6: 17 residues within 4Å: Chain C: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, W.532, R.533, P.534, G.535, S.536, G.537, F.538, T.539 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.449, C:K.450, C:S.451, C:R.453, C:S.454, C:S.454, C:G.531, C:R.533, C:G.535, C:S.536, C:G.537, C:F.538 Water bridges: C:R.472, C:R.506, C:T.539 Salt bridges: C:K.450, C:R.506 FBP.8: 17 residues within 4Å: Chain D: L.448, T.449, K.450, S.451, R.453, S.454, W.499, R.506, G.531, W.532, R.533, P.534, G.535, S.536, G.537, F.538, T.539 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.449, D:K.450, D:S.451, D:R.453, D:S.454, D:S.454, D:G.531, D:R.533, D:G.535, D:S.536, D:G.537, D:F.538 Water bridges: D:R.472, D:R.506, D:T.539 Salt bridges: D:K.450, D:R.506

4 x THR: THREONINE(Non-covalent)

THR.2: 10 residues within 4Å: Chain A: R.60, N.61, T.62, G.63, N.87, R.123, H.481, I.486, F.487, P.488 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:N.87, A:N.87, A:H.481, A:I.486, T.2, T.2, T.2 Salt bridges: A:R.123, A:H.481 THR.4: 10 residues within 4Å: Chain B: R.60, N.61, T.62, G.63, N.87, R.123, H.481, I.486, F.487, P.488 9 PLIP interactions: 3 Ligand-Ligand interactions, 6 interactions with chain B Hydrogen bonds: T.4, T.4, T.4, B:N.87, B:N.87, B:H.481, B:I.486 Salt bridges: B:R.123, B:H.481 THR.5: 10 residues within 4Å: Chain C: R.60, N.61, T.62, G.63, N.87, R.123, H.481, I.486, F.487, P.488 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:N.87, C:H.481, T.5, T.5 Salt bridges: C:R.123, C:H.481 THR.7: 10 residues within 4Å: Chain D: R.60, N.61, T.62, G.63, N.87, R.123, H.481, I.486, F.487, P.488 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.87, D:H.481, T.7, T.7 Salt bridges: D:R.123, D:H.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saur, M. et al., Fragment-based drug discovery using cryo-EM. Drug Discov Today (2020)

Release Date

2020-01-15

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM

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