SMTL ID : 8f5u.1

Rabbit muscle pyruvate kinase in complex with magnesium, potassium and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.118, I.119, R.120, G.208, V.209, F.244, D.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.119, A:R.120, A:V.209 Water bridges: A:R.120 GOL.3: 6 residues within 4Å: Chain A: P.117, N.210, L.211, V.216, R.246, E.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.117, A:N.210, A:L.211, A:R.246, A:E.300 GOL.10: 8 residues within 4Å: Chain B: P.117, V.209, N.210, L.211, V.216, R.246, E.300 Ligands: GOL.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.117, B:N.210, B:L.211, B:R.246, B:R.246 GOL.15: 4 residues within 4Å: Chain B: D.407, E.410, Q.440, R.443 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.405, B:E.410, B:R.443, B:R.443 Water bridges: B:Q.440 GOL.16: 9 residues within 4Å: Chain B: E.118, I.119, R.120, G.208, V.209, N.210, F.244, D.296 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.119, B:R.120, B:V.209, B:N.210, B:D.296 GOL.21: 4 residues within 4Å: Chain C: D.407, E.410, Q.440, R.443 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.407, C:D.407, C:R.443, C:R.443 Water bridges: C:A.320, C:Q.440 GOL.22: 6 residues within 4Å: Chain D: R.43, K.66, S.67, G.68, R.106, H.379 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.43, D:R.106, D:H.379 GOL.26: 7 residues within 4Å: Chain D: G.213, A.214, A.215, H.274, E.275, R.278, R.279 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.213, D:G.213, D:R.278 Water bridges: D:G.213

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

EDO.2: 5 residues within 4Å: Chain A: E.285, A.286, S.287, D.288, K.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.255, A:A.286, A:K.322 EDO.4: 5 residues within 4Å: Chain A: R.339, P.340, R.342 Chain B: D.178, Q.329 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.342, A:R.342, B:D.178, B:Q.329 Water bridges: A:R.339, A:P.340

8 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: T.432, S.434, S.437 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.432, A:S.437 K.6: 5 residues within 4Å: Chain A: N.75, S.77, D.113, T.114, S.243 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.77, A:D.113, A:T.114, H2O.3, H2O.8 K.11: 6 residues within 4Å: Chain B: N.75, S.77, D.113, T.114, S.243, K.270 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.77, B:D.113, B:T.114, H2O.14, H2O.16 K.12: 3 residues within 4Å: Chain B: T.432, S.434, S.437 No protein-ligand interaction detected (PLIP) K.17: 5 residues within 4Å: Chain C: N.75, S.77, D.113, T.114, K.270 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.77, C:D.113, C:T.114, H2O.24, H2O.29 K.18: 3 residues within 4Å: Chain C: T.432, S.434, S.437 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.432 K.23: 5 residues within 4Å: Chain D: N.75, S.77, D.113, T.114, K.270 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.77, D:D.113, D:T.114 K.24: 2 residues within 4Å: Chain D: T.432, S.437 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.432, D:S.437

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: E.272, D.296 Ligands: PYR.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.1, H2O.2 MG.13: 3 residues within 4Å: Chain B: E.272, D.296 Ligands: PYR.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.272, B:D.296, H2O.12, H2O.12 MG.19: 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.22, H2O.26, H2O.28 MG.25: 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.36, H2O.37, H2O.38

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.8: 8 residues within 4Å: Chain A: K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.270, A:G.295, A:D.296, A:T.328 PYR.14: 9 residues within 4Å: Chain B: K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328 Ligands: MG.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.293 Hydrogen bonds: B:K.270, B:G.295, B:D.296 Water bridges: B:R.73 Salt bridges: B:K.270

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

TRS.9: 10 residues within 4Å: Chain A: R.43, N.44, T.45, G.46, N.70, H.464, G.468, I.469, F.470, P.471 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.45, A:H.464, A:G.468 Water bridges: A:R.500 TRS.20: 11 residues within 4Å: Chain C: R.43, N.44, T.45, G.46, N.70, H.464, Y.466, G.468, I.469, F.470, P.471 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.43, C:T.45, C:H.464, C:H.464

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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