SMTL ID : 8f5t.1 (1 other biounit)

Rabbit muscle pyruvate kinase in complex with sodium and magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.272, D.296 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.4, H2O.6, H2O.7, H2O.8 MG.4: 2 residues within 4Å: Chain B: E.272, D.296 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.272, B:D.296, H2O.12, H2O.17, H2O.18 MG.7: 2 residues within 4Å: Chain C: E.272, D.296 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.272, H2O.21, H2O.21, H2O.23, H2O.28 MG.9: 2 residues within 4Å: Chain D: E.272, D.296 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.272, D:D.296, H2O.35, H2O.35, H2O.36

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

NA.2: 3 residues within 4Å: Chain A: T.432, S.434, S.437 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.432, A:R.436, A:S.437, A:S.437 Water bridges: A:S.434, A:R.436 NA.5: 3 residues within 4Å: Chain B: T.432, S.434, S.437 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.432, B:R.436, B:S.437, B:S.437 Water bridges: B:E.433, B:R.436 NA.8: 3 residues within 4Å: Chain C: T.432, S.434, S.437 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.436, C:S.437, C:S.437 Water bridges: C:S.434 NA.10: 4 residues within 4Å: Chain D: T.432, S.434, R.436, S.437 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.436, D:S.437 Water bridges: D:E.433, D:R.436, D:S.437, D:G.520

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 11 residues within 4Å: Chain A: R.43, N.44, T.45, G.46, N.70, H.464, Y.466, G.468, I.469, F.470, P.471 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.43, A:N.44, A:N.70, A:H.464, A:H.464 TRS.11: 11 residues within 4Å: Chain D: R.43, N.44, T.45, G.46, N.70, R.106, H.464, Y.466, I.469, F.470, P.471 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.43, D:N.44, D:T.45, D:N.70, D:R.106, D:H.464, D:G.468

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain B: S.405, D.407, E.410, Q.440, R.443 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.405, B:D.407, B:R.443 Water bridges: B:Q.440, B:R.443, B:R.443 GOL.12: 5 residues within 4Å: Chain D: G.321, R.436, H.439, Q.440, Y.466 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.439, D:Q.440, D:Y.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swint-Kruse, L. et al., PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) (2023)

Release Date

2023-05-24

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM

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