SMTL ID : 8xfd.1

Crystal structure of pyruvate kinase tetramer in complex with allosteric activator, Mitapivat (MTPV, AG-348)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.284, D.308 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.284, A:D.308, H2O.5 MG.3: 2 residues within 4Å: Chain B: E.284, D.308 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.284, B:D.308 MG.6: 2 residues within 4Å: Chain C: E.284, D.308 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.284, C:D.308, H2O.19, H2O.22 MG.8: 2 residues within 4Å: Chain D: E.284, D.308 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.284, D:D.308

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

FBP.2: 16 residues within 4Å: Chain A: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, G.526, R.528, P.529, G.530, S.531, G.532, Y.533, T.534 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.444, A:T.444, A:T.445, A:T.446, A:G.447, A:R.448, A:S.449, A:S.449, A:S.449, A:G.526, A:R.528, A:G.530, A:G.532, A:Y.533 Water bridges: A:T.445, A:T.445, A:R.501, A:G.526, A:T.534, A:T.534 Salt bridges: A:R.501 FBP.4: 16 residues within 4Å: Chain B: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, G.526, R.528, P.529, G.530, S.531, G.532, Y.533, T.534 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.444, B:T.445, B:T.445, B:T.446, B:R.448, B:S.449, B:S.449, B:G.526, B:G.530, B:G.532, B:Y.533, B:Y.533 Water bridges: B:R.501, B:R.501, B:T.534 Salt bridges: B:R.501 FBP.7: 16 residues within 4Å: Chain C: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, G.526, R.528, P.529, G.530, S.531, G.532, Y.533, T.534 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.444, C:T.445, C:T.446, C:G.447, C:S.449, C:S.449, C:G.526, C:G.530, C:G.532, C:Y.533, C:Y.533 Water bridges: C:L.443, C:W.494, C:R.501, C:R.501, C:R.501, C:T.534 Salt bridges: C:R.501 FBP.9: 16 residues within 4Å: Chain D: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, G.526, R.528, P.529, G.530, S.531, G.532, Y.533, T.534 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:T.444, D:T.444, D:T.445, D:T.446, D:R.448, D:S.449, D:S.449, D:G.526, D:R.528, D:R.528, D:G.530, D:G.532, D:Y.533 Water bridges: D:L.443, D:L.443, D:T.445, D:R.448, D:R.467, D:W.494, D:D.497, D:R.501, D:R.501, D:G.526 Salt bridges: D:R.501

2 x WV2: mitapivat

WV2.5: 19 residues within 4Å: Chain A: F.38, L.39, L.42, K.323, L.365, D.366, V.401, Y.402, L.406 Chain B: F.38, L.42, N.330, L.365, D.366, V.401, Y.402, Q.405, L.406, E.409 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.38, B:F.38, B:L.365, B:L.365, B:Q.405, B:L.406, B:L.406, A:F.38, A:L.39, A:L.39, A:L.42, A:V.401, A:L.406 Hydrogen bonds: B:L.365, B:Y.402, A:D.366 WV2.10: 17 residues within 4Å: Chain C: F.38, L.39, L.42, K.323, L.365, D.366, V.401, Y.402 Chain D: F.38, L.42, L.365, D.366, V.401, Y.402, Q.405, L.406, E.409 15 PLIP interactions: 6 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:F.38, C:L.39, C:L.42, C:V.401, C:Y.402, D:F.38, D:F.38, D:L.365, D:L.365, D:Q.405, D:L.406, D:L.406 Water bridges: C:K.323 Hydrogen bonds: D:L.365, D:Y.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/AG-348. Crystals (2024)

Release Date

2024-05-15

Peptides

Isoform L-type of Pyruvate kinase PKLR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoform L-type of Pyruvate kinase PKLR