SMTL ID : 6nn4.1

The structure of human liver pyruvate kinase, hLPYK-D499N, in complex with Fru-1,6-BP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 20 residues within 4Å: Chain A: L.443, T.444, T.445, T.446, G.447, R.448, S.449, W.494, V.498, R.501, T.525, G.526, W.527, 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.445, A:T.446, A:T.446, A:R.448, A:S.449, A:S.449, A:S.449, A:W.494, A:G.526, A:R.528, A:G.530, A:G.530, A:S.531, A:S.531, A:G.532, A:Y.533 Water bridges: A:R.501, A:R.501, A:R.501 Salt bridges: A:R.501 FBP.5: 21 residues within 4Å: Chain B: L.443, T.444, T.445, T.446, G.447, R.448, S.449, R.467, W.494, V.498, R.501, T.525, G.526, W.527, R.528, P.529, G.530, S.531, G.532, Y.533, T.534 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.444, B:T.444, B:T.445, B:T.445, B:T.446, B:T.446, B:R.448, B:S.449, B:S.449, B:W.494, B:G.526, B:R.528, B:G.530, B:G.530, B:G.532, B:Y.533 Water bridges: B:R.501 Salt bridges: B:R.501 FBP.8: 18 residues within 4Å: Chain C: L.443, T.444, T.445, T.446, G.447, R.448, S.449, W.494, V.498, R.501, T.525, G.526, W.527, R.528, P.529, G.532, Y.533, T.534 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.444, C:T.445, C:T.445, C:T.446, C:T.446, C:R.448, C:S.449, C:S.449, C:S.449, C:W.494, C:G.526, C:R.528, C:G.532, C:G.532, C:Y.533 Salt bridges: C:R.501 FBP.11: 19 residues within 4Å: Chain D: L.443, T.444, T.445, T.446, G.447, R.448, S.449, W.494, V.498, R.501, T.525, G.526, W.527, R.528, P.529, G.530, G.532, Y.533, T.534 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:T.444, D:T.444, D:T.445, D:T.446, D:T.446, D:R.448, D:S.449, D:S.449, D:W.494, D:G.526, D:R.528, D:G.530, D:G.530, D:G.532, D:G.532, D:Y.533 Water bridges: D:R.501 Salt bridges: D:R.501

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

EDO.2: 8 residues within 4Å: Chain A: A.33, M.34, H.403, R.404, F.433, R.459 Chain D: R.411, L.416 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.404, A:R.459, A:R.459 Water bridges: A:H.403 EDO.3: 2 residues within 4Å: Chain A: H.90, G.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.91 EDO.6: 5 residues within 4Å: Chain B: A.33, H.403, R.404, F.433, R.459 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.459, B:R.459 Water bridges: B:A.33, B:R.404 EDO.9: 7 residues within 4Å: Chain B: R.411 Chain C: A.33, M.34, H.403, R.404, F.433, R.459 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.459, B:R.411, B:R.411 EDO.12: 5 residues within 4Å: Chain D: A.54, R.55, H.391, F.482, F.514 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.55, D:R.55 EDO.13: 11 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:S.454, D:R.457 Water bridges: D:R.457 EDO.14: 6 residues within 4Å: Chain A: R.411 Chain D: A.33, H.403, R.404, F.433, R.459 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.411, D:R.459, D:R.459

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.4: 12 residues within 4Å: Chain A: R.85, N.87, D.125, K.282, E.284, A.305, R.306, G.307, D.308, L.309, T.340, S.374 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.87, A:G.307, A:D.308, A:T.340, A:T.340 Water bridges: A:R.85, A:R.85, A:K.282 Salt bridges: A:R.85, A:K.282 PEP.7: 11 residues within 4Å: Chain B: R.85, N.87, D.125, K.282, E.284, A.305, R.306, G.307, D.308, L.309, T.340 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.87, B:D.125, B:E.284, B:G.307, B:D.308, B:D.308, B:T.340 Water bridges: B:S.255, B:T.340 Salt bridges: B:R.85, B:K.282 PEP.10: 10 residues within 4Å: Chain C: R.85, N.87, K.282, E.284, A.305, R.306, G.307, D.308, L.309, T.340 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.284, C:G.307, C:D.308, C:D.308, C:T.340, C:T.340 Water bridges: C:S.255 Salt bridges: C:R.85, C:K.282 PEP.15: 10 residues within 4Å: Chain D: R.85, N.87, K.282, E.284, A.305, R.306, G.307, D.308, L.309, T.340 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.87, D:G.307, D:D.308, D:D.308, D:T.340, D:T.340 Water bridges: D:S.255 Salt bridges: D:R.85, D:K.282

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