SMTL ID : 8f5t.2 (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 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.4, H2O.6, H2O.6 MG.5: 2 residues within 4Å: Chain B: E.272, D.296 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.296, H2O.10, H2O.12, H2O.12, H2O.13 MG.8: 2 residues within 4Å: Chain C: E.272, D.296 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.272, C:D.296, H2O.14, H2O.16, H2O.18 MG.11: 2 residues within 4Å: Chain D: E.272, D.296 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.272, D:E.272, D:D.296, H2O.21, H2O.23

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

NA.2: 4 residues within 4Å: Chain A: T.432, S.434, R.436, S.437 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.432, A:S.434, A:R.436, A:S.437 Water bridges: A:S.434, A:R.436 NA.6: 4 residues within 4Å: Chain B: T.432, S.434, R.436, S.437 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.436, B:S.437, B:S.437 Water bridges: B:E.433 NA.9: 3 residues within 4Å: Chain C: T.432, S.434, S.437 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.432, C:S.434, C:R.436, C:S.437 Water bridges: C:E.433, C:S.434 NA.12: 3 residues within 4Å: Chain D: T.432, S.434, S.437 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.432, D:S.437

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

TRS.3: 10 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.44, A:N.70, A:N.70, A:H.464, A:H.464, A:G.468 TRS.7: 10 residues within 4Å: Chain B: R.43, N.44, T.45, G.46, N.70, H.464, Y.466, I.469, F.470, P.471 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.43, B:R.43, B:N.44, B:H.464 TRS.10: 10 residues within 4Å: Chain C: R.43, N.44, T.45, G.46, N.70, H.464, Y.466, I.469, F.470, P.471 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.43, C:N.70, C:H.464, C:H.464, C:G.468, C:I.469 Water bridges: C:R.43 TRS.13: 11 residues within 4Å: Chain D: 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 D Hydrogen bonds: D:R.43, D:N.44, D:N.70, D:H.464 Water bridges: D:R.43

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.321, R.436, H.439, Q.440, Y.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.439, A:Q.440 Water bridges: A:G.321

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
E

B
F

C
G

D
H

Pyruvate kinase PKM

Related Entries With Identical Sequence