SMTL ID : 6nn5.1

The structure of human liver pyruvate kinase, hLPYK-W527H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: T.421, T.444, T.445, T.446, G.447, R.448, S.449, G.532, Y.533, T.534 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.445, A:T.446, A:T.446, A:G.447, A:G.532 GOL.2: 9 residues within 4Å: Chain A: R.85, F.256, K.282, E.284, A.305, R.306, G.307, D.308, T.340 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.85, A:K.282, A:G.307, A:D.308, A:D.308, A:T.340, A:T.340 GOL.3: 7 residues within 4Å: Chain A: A.33, M.34, H.403, R.404, F.433, R.459 Chain C: R.411 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.404, A:R.459, A:R.459, C:R.411 GOL.4: 8 residues within 4Å: Chain A: H.527, R.528, S.531, N.535 Chain C: R.538, V.539, L.540, S.541 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.528, A:N.535, C:R.538, C:R.538, C:S.541 GOL.8: 9 residues within 4Å: Chain B: T.421, T.444, T.445, T.446, G.447, R.448, S.449, G.532, T.534 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.445, B:T.446, B:T.446, B:S.449, B:G.532 GOL.9: 9 residues within 4Å: Chain B: R.85, K.282, E.284, A.305, R.306, G.307, D.308, L.309, T.340 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.85, B:K.282, B:G.307, B:D.308, B:D.308, B:D.308, B:T.340 GOL.12: 1 residues within 4Å: Chain C: E.94 No protein-ligand interaction detected (PLIP) GOL.13: 9 residues within 4Å: Chain C: T.444, T.445, T.446, G.447, R.448, S.449, G.532, Y.533, T.534 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.444, C:T.445, C:T.446, C:R.448, C:S.449, C:G.532 GOL.14: 11 residues within 4Å: Chain C: R.85, N.87, K.282, E.284, A.305, R.306, G.307, D.308, A.339, T.340, M.372 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.85, C:K.282, C:G.307, C:D.308, C:T.340, C:T.340 GOL.18: 6 residues within 4Å: Chain D: A.54, R.55, G.80, R.118, H.391, F.482 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.55, D:R.55 Water bridges: D:R.55 GOL.19: 11 residues within 4Å: Chain D: R.85, N.87, K.282, E.284, A.305, R.306, G.307, D.308, L.309, A.339, T.340 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.85, D:K.282, D:G.307, D:D.308, D:D.308, D:D.308, D:T.340 Water bridges: D:N.87 GOL.20: 11 residues within 4Å: Chain D: T.421, T.444, T.445, T.446, G.447, R.448, S.449, G.532, Y.533, T.534 Ligands: EDO.21 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.444, D:T.444, D:T.445, D:T.445, D:T.446, D:G.532

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

EDO.5: 6 residues within 4Å: Chain A: D.293, E.294, L.296, E.297, A.332, K.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.293 EDO.6: 10 residues within 4Å: Chain A: K.278, D.300, P.335, T.446, G.447, Q.451, Q.474, V.475, L.477, C.478 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.278 EDO.7: 10 residues within 4Å: Chain A: F.38, K.323, N.362, L.365, D.366 Chain D: F.38, L.42, K.323, N.362, L.365 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.323 Water bridges: D:N.362 EDO.10: 11 residues within 4Å: Chain B: G.333, K.334, P.335, D.369, Q.451, S.454, R.455, R.457, L.477, C.478, R.479 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.454, B:R.457, B:L.477 EDO.11: 7 residues within 4Å: Chain B: V.263, A.264, R.267, I.279, V.298, S.299, D.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.267, B:R.267, B:D.300 EDO.15: 6 residues within 4Å: Chain C: A.97, E.98, I.100, A.101, R.104, H.247 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.101 EDO.16: 10 residues within 4Å: Chain B: F.38, L.39, L.42 Chain C: I.326, G.327, N.330, L.365, D.366, G.367, L.406 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.330 EDO.17: 10 residues within 4Å: Chain C: K.278, P.335, T.446, G.447, R.448, Q.451, Q.474, V.475, L.477, C.478 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.278, C:G.447 EDO.21: 9 residues within 4Å: Chain D: T.445, W.494, V.498, R.501, P.529, G.530, S.531, G.532 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.494, D:R.501, D:R.501 EDO.22: 6 residues within 4Å: Chain D: R.72, N.381, F.382, P.383, V.384, E.385 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.384, D:E.385, D:E.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McFarlane, J.S. et al., Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-pi bond. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-06-19

Peptides

Pyruvate kinase PKLR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKLR