SMTL ID : 7r6y.1

E117K mutant pyruvate kinase from rabbit muscle

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: R.43, N.44, G.46, N.70, H.464, Y.466, I.469, P.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.44 Salt bridges: A:H.464 ACT.2: 8 residues within 4Å: Chain A: T.432, E.433, S.434, G.435, R.436, S.437, G.520, F.521 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.432, A:E.433, A:S.434, A:G.435, A:R.436, A:S.437, A:S.437 ACT.5: 5 residues within 4Å: Chain B: R.43, N.44, N.70, H.464, I.469 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.43 Salt bridges: B:H.464 ACT.6: 6 residues within 4Å: Chain B: T.432, E.433, S.434, R.436, S.437, G.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.433, B:S.434, B:S.437 ACT.9: 7 residues within 4Å: Chain C: R.43, N.44, G.46, N.70, R.106, H.464, I.469 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.43, C:R.106, C:H.464 ACT.10: 7 residues within 4Å: Chain C: T.432, E.433, S.434, R.436, S.437, G.520, F.521 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.433, C:S.434, C:R.436, C:S.437 ACT.13: 8 residues within 4Å: Chain D: R.43, N.44, G.46, N.70, H.464, Y.466, I.469, P.471 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.44 Water bridges: D:R.43 Salt bridges: D:R.43, D:H.464 ACT.14: 7 residues within 4Å: Chain D: T.432, E.433, S.434, R.436, S.437, G.520 Ligands: ACT.15 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:R.436 Hydrogen bonds: D:T.432, D:E.433, D:S.434, D:S.437, D:S.437 ACT.15: 5 residues within 4Å: Chain D: L.431, E.433, G.514, F.521 Ligands: ACT.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.433 Hydrogen bonds: D:G.514

4 x OXL: OXALATE ION(Non-covalent)

OXL.3: 9 residues within 4Å: Chain A: K.270, M.291, A.293, R.294, G.295, D.296, T.328, M.360 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.295, A:D.296, A:T.328 Water bridges: A:S.243, A:K.270 Salt bridges: A:R.73, A:K.270 OXL.7: 8 residues within 4Å: Chain B: K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.295, B:D.296, B:T.328, B:T.328 Water bridges: B:K.270, B:K.270, B:K.270, B:S.362 Salt bridges: B:K.270 OXL.11: 9 residues within 4Å: Chain C: R.73, K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MG.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.295, C:D.296 Water bridges: C:S.243, C:K.270 Salt bridges: C:R.73, C:K.270, C:K.270 OXL.16: 10 residues within 4Å: Chain D: R.73, K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328 Ligands: MG.17 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.295, D:D.296, D:D.296 Water bridges: D:K.270, D:K.270 Salt bridges: D:R.73, D:K.270

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.272, D.296 Ligands: OXL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.1 MG.8: 4 residues within 4Å: Chain B: K.118, E.272, D.296 Ligands: OXL.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.272, B:D.296, H2O.10, H2O.11 MG.12: 4 residues within 4Å: Chain C: K.270, E.272, D.296 Ligands: OXL.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.272, C:D.296, H2O.15, H2O.15 MG.17: 4 residues within 4Å: Chain D: K.270, E.272, D.296 Ligands: OXL.16 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.272, D:D.296, H2O.20, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez-Silva, L. et al., The K + -Dependent and -Independent Pyruvate Kinases Acquire the Active Conformation by Different Mechanisms. Int J Mol Sci (2022)

Release Date

2022-05-25

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM