SMTL ID : 4ip7.1

Structure of the S12D variant of human liver pyruvate kinase in complex with citrate and FBP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: E.284, D.308 Ligands: FLC.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.284, A:D.308, H2O.1, H2O.12 MN.8: 3 residues within 4Å: Chain B: E.284, D.308 Ligands: FLC.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.284, B:D.308, H2O.15, H2O.16 MN.16: 3 residues within 4Å: Chain C: E.284, D.308 Ligands: FLC.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.284, C:D.308, H2O.27, H2O.29 MN.23: 3 residues within 4Å: Chain D: E.284, D.308 Ligands: FLC.24 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.284, D:D.308, H2O.40, H2O.42

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 13 residues within 4Å: Chain A: R.85, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.1, NA.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.305 Hydrogen bonds: A:K.282, A:G.307, A:D.308, A:T.340 Water bridges: A:R.85, A:N.87, A:N.87, A:S.374, A:S.374 Salt bridges: A:R.85, A:R.85, A:K.282, A:K.282 FLC.9: 13 residues within 4Å: Chain B: R.85, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.8, NA.14 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.305 Hydrogen bonds: B:K.282, B:G.307, B:D.308 Water bridges: B:N.87, B:N.87, B:N.87, B:T.340, B:S.374 Salt bridges: B:R.85, B:R.85, B:K.282, B:K.282 FLC.17: 13 residues within 4Å: Chain C: R.85, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.16, NA.22 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.305 Hydrogen bonds: C:K.282, C:G.307, C:D.308, C:T.340 Water bridges: C:N.87, C:S.89, C:S.89, C:K.282, C:T.340, C:S.374 Salt bridges: C:R.85, C:R.85, C:K.282, C:K.282 FLC.24: 13 residues within 4Å: Chain D: R.85, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.23, NA.30 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:A.305 Hydrogen bonds: D:K.282, D:G.307, D:D.308, D:T.340, D:T.340 Water bridges: D:N.87, D:N.87, D:S.89, D:S.89, D:S.255 Salt bridges: D:R.85, D:R.85, D:K.282, D:K.282

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

FBP.3: 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 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:T.444, A:T.444, A:T.445, A:T.445, A:T.446, A:G.447, A:R.448, A:S.449, A:S.449, A:G.526, A:R.528, A:R.528, A:G.530, A:G.532, A:Y.533 Water bridges: A:R.467, A:R.467, A:R.501, A:R.501, A:G.526, A:T.534, A:T.534 Salt bridges: A:R.501 FBP.10: 17 residues within 4Å: Chain B: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, 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 B Hydrogen bonds: B:T.444, B:T.445, B:T.445, B:T.446, B:G.447, B:S.449, B:S.449, B:G.526, B:R.528, B:R.528, B:G.530, B:G.532, B:Y.533 Water bridges: B:R.467, B:W.494, B:R.501, B:R.501, B:R.501, B:G.526, B:T.534 Salt bridges: B:R.501 FBP.18: 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 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.444, C:T.445, C:T.445, C:T.446, C:S.449, C:S.449, C:S.449, C:G.526, C:R.528, C:G.530, C:G.532, C:Y.533 Water bridges: C:W.494, C:D.497, C:R.501, C:R.501, C:R.501, C:G.526, C:T.534 Salt bridges: C:R.501 FBP.25: 17 residues within 4Å: Chain D: L.443, T.444, T.445, T.446, R.448, S.449, W.494, R.501, 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 D Hydrogen bonds: D:T.444, D:T.445, D:T.446, D:G.447, 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:T.445, D:T.445, D:W.494, D:D.497, D:R.501, D:R.501, D:G.526, D:T.534 Salt bridges: D:R.501

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

EDO.4: 9 residues within 4Å: Chain A: G.333, K.334, P.335, D.369, Q.451, S.454, R.455, R.457, C.478 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.454, A:R.457, A:L.477 Water bridges: A:R.457 EDO.5: 4 residues within 4Å: Chain A: K.278, Q.451, Q.474, C.478 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.278 Water bridges: A:D.300, A:Q.451 EDO.11: 9 residues within 4Å: Chain B: G.333, K.334, P.335, D.369, Q.451, S.454, R.455, R.457, C.478 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.369, B:S.454, B:R.457 EDO.13: 8 residues within 4Å: Chain B: R.55, S.56, T.57, S.58, H.476, G.480, V.481, F.482 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.476, B:G.480 Water bridges: B:S.58, B:D.369 EDO.15: 7 residues within 4Å: Chain A: D.190, L.192, Q.341 Chain C: R.351, P.352, T.353, R.354 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:Q.341, C:R.354, C:R.354 Water bridges: A:D.190, C:K.349, C:R.351, C:P.352 EDO.21: 1 residues within 4Å: Chain C: H.93 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.93 EDO.27: 9 residues within 4Å: Chain D: G.333, K.334, P.335, D.369, Q.451, S.454, R.455, R.457, C.478 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.454, D:R.457 EDO.28: 6 residues within 4Å: Chain D: R.267, E.297, V.298, S.299, D.300, K.334 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.267, D:D.300, D:K.334, D:K.334 Water bridges: D:D.300, D:D.300 EDO.29: 5 residues within 4Å: Chain D: K.278, Q.451, Q.474, V.475, C.478 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.474 Water bridges: D:K.278, D:D.300, D:Q.451

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 7 residues within 4Å: Chain A: R.411 Chain B: A.33, H.403, R.404, F.407, F.433, R.459 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.411, A:R.411, B:R.459, B:R.459 Water bridges: B:R.404 PEG.12: 2 residues within 4Å: Chain B: H.93, F.243 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.93 Water bridges: B:H.93, B:H.93

4 x NA: SODIUM ION(Non-functional Binders)

NA.7: 7 residues within 4Å: Chain A: R.85, N.87, S.89, D.125, T.126, K.282 Ligands: FLC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.85, A:D.125 Water bridges: A:S.255 NA.14: 7 residues within 4Å: Chain B: R.85, N.87, S.89, D.125, T.126, K.282 Ligands: FLC.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.85, B:D.125 NA.22: 7 residues within 4Å: Chain C: R.85, N.87, S.89, D.125, T.126, K.282 Ligands: FLC.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.85, C:N.87 Water bridges: C:S.255 NA.30: 7 residues within 4Å: Chain D: R.85, N.87, S.89, D.125, T.126, K.282 Ligands: FLC.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.85, D:T.126 Water bridges: D:N.87, D:S.255

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.19: 2 residues within 4Å: Chain C: H.90, G.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.91 Water bridges: C:Y.95 1PE.20: 13 residues within 4Å: Chain C: R.55, S.56, T.57, S.58, N.82, D.369, H.476, L.477, C.478, R.479, G.480, V.481, F.482 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.55, C:S.58, C:D.369, C:V.481 Water bridges: C:N.82, C:V.481, C:V.481

1 x ADN: ADENOSINE(Non-covalent)

ADN.26: 2 residues within 4Å: Chain D: E.98, N.102 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.102, D:N.102 Water bridges: D:R.68, D:E.98, D:E.98 pi-Cation interactions: D:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holyoak, T. et al., Energetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase. Biochemistry (2013)

Release Date

2013-01-30

Peptides

Pyruvate kinase isozymes L: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes L