SMTL ID : 4ima.1

The structure of C436M-hLPYK in complex with Citrate/Mn/ATP/Fru-1,6-BP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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.8, H2O.8 MN.4: 3 residues within 4Å: Chain B: E.284, D.308 Ligands: FLC.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.284, B:D.308, H2O.16, H2O.16 MN.8: 3 residues within 4Å: Chain C: E.284, D.308 Ligands: FLC.9 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.284, C:D.308, H2O.19, H2O.25 MN.11: 3 residues within 4Å: Chain D: E.284, D.308 Ligands: FLC.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.284, D:D.308, H2O.33, H2O.33

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 12 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.305 Hydrogen bonds: A:N.87, A:K.282, A:G.307, A:D.308, A:T.340 Water bridges: A:S.255 Salt bridges: A:R.85, A:R.85, A:K.282, A:K.282 FLC.5: 13 residues within 4Å: Chain B: R.85, N.87, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.305 Hydrogen bonds: B:N.87, B:K.282, B:G.307, B:D.308, B:S.374, B:S.374 Water bridges: B:S.89, B:S.255 Salt bridges: B:R.85, B:R.85, B:K.282, B:K.282 FLC.9: 12 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.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.305 Hydrogen bonds: C:N.87, C:K.282, C:G.307, C:D.308, C:T.340 Water bridges: C:S.89, C:T.340 Salt bridges: C:R.85, C:R.85, C:K.282, C:K.282 FLC.12: 13 residues within 4Å: Chain D: R.85, N.87, D.125, K.282, E.284, M.303, A.305, R.306, G.307, D.308, T.340, M.372 Ligands: MN.11 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.87, D:K.282, D:G.307, D:D.308, D:T.340, D:T.340, D:S.374 Water bridges: 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: 17 residues within 4Å: Chain A: 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 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:T.444, A:T.444, A:T.445, A:T.446, A:S.449, A:S.449, A:S.449, A:G.526, A:R.528, A:G.530, A:G.532, A:Y.533, A:T.534 Water bridges: A:T.445, A:T.445, A:R.467, A:D.497, A:R.501, A:R.501, A:R.501, A:G.526, A:T.534 Salt bridges: A:R.501 FBP.6: 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.444, B:T.445, B:T.445, B:T.446, 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:G.526 Salt bridges: B:R.501 FBP.10: 17 residues within 4Å: Chain C: 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 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:T.444, C:T.445, C:T.445, C:T.446, C:G.447, C:S.449, C:S.449, C:G.526, C:R.528, 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:R.501, C:G.526, C:T.534 Salt bridges: C:R.501 FBP.13: 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 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:T.444, D:T.445, D:T.446, D:S.449, D:S.449, D:G.526, D:R.528, D:G.530, D:G.532, D:Y.533 Water bridges: D:T.445, D:T.445, D:R.467, D:R.501, D:R.501, D:R.501, D:R.501, D:G.526, D:T.534 Salt bridges: D:R.501

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

EDO.7: 7 residues within 4Å: Chain B: S.56, S.58, N.82, H.476, C.478, V.481, F.482 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.476, B:C.478

1 x ADN: ADENOSINE(Non-covalent)

ADN.14: 3 residues within 4Å: Chain D: R.68, E.98, N.102 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.68, D:E.98, D:N.102, D:N.102 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

2013-01-23

Peptides

Pyruvate kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase