SMTL ID : 3n25.1 (1 other biounit)

The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

4 x PRO: PROLINE(Non-covalent)

PRO.1: 10 residues within 4Å: Chain A: R.43, N.44, N.70, R.106, H.464, Y.466, G.468, I.469, F.470, P.471 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.70, A:H.464, A:I.469, A:I.469, P.1, P.1 Salt bridges: A:R.43, A:R.106, A:H.464 PRO.13: 9 residues within 4Å: Chain B: R.43, N.44, G.46, N.70, H.464, Y.466, I.469, F.470, P.471 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.70, B:H.464, B:I.469, B:I.469, P.13, P.13 Salt bridges: B:R.43, B:H.464 PRO.23: 11 residues within 4Å: Chain C: R.43, N.44, T.45, G.46, N.70, R.106, H.464, Y.466, I.469, F.470, P.471 8 PLIP interactions: 6 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:N.70, C:I.469, C:I.469, P.23, P.23 Water bridges: C:R.106 Salt bridges: C:R.106, C:H.464 PRO.31: 10 residues within 4Å: Chain D: R.43, N.44, N.70, R.106, H.464, Y.466, G.468, I.469, F.470, P.471 8 PLIP interactions: 6 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.70, D:H.464, D:I.469, D:I.469, P.31, P.31 Salt bridges: D:R.106, D:H.464

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: E.272, D.296 Ligands: PYR.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.5, H2O.7 MN.14: 4 residues within 4Å: Chain B: K.270, E.272, D.296 Ligands: PYR.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.272, B:D.296, H2O.10, H2O.12 MN.24: 4 residues within 4Å: Chain C: K.270, E.272, D.296 Ligands: PYR.25 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.272, C:D.296, H2O.18, H2O.19 MN.33: 3 residues within 4Å: Chain D: E.272, D.296 Ligands: PYR.34 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.272, D:D.296, H2O.25

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 10 residues within 4Å: Chain A: R.73, K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.270, A:G.295, A:D.296 Water bridges: A:R.73 PYR.15: 12 residues within 4Å: Chain B: R.73, K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328, M.360 Ligands: MN.14, EDO.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.270, B:G.295, B:D.296 Salt bridges: B:K.270 PYR.25: 10 residues within 4Å: Chain C: K.270, E.272, M.291, A.293, R.294, G.295, D.296, T.328, M.360 Ligands: MN.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.270, C:G.295, C:D.296 Water bridges: C:R.73 PYR.34: 10 residues within 4Å: Chain D: R.73, K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MN.33, EDO.40 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.270, D:G.295, D:D.296, D:T.328 Salt bridges: D:K.270

4 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.75, S.77, D.113, T.114, S.243, K.270 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.77, A:D.113, A:T.114, H2O.1, H2O.3 K.16: 5 residues within 4Å: Chain B: N.75, S.77, D.113, T.114, S.243 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.77, B:D.113 K.26: 6 residues within 4Å: Chain C: N.75, S.77, D.113, T.114, S.243, K.270 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.77, C:D.113, C:T.114, H2O.17 K.35: 6 residues within 4Å: Chain D: N.75, S.77, D.113, T.114, S.243, K.270 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.77, D:D.113

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

NA.5: 7 residues within 4Å: Chain A: I.124, K.125, G.126, S.127, G.128, T.129, A.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.126 NA.6: 3 residues within 4Å: Chain A: T.432, S.434, S.437 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.432, A:T.432, A:S.437 NA.17: 3 residues within 4Å: Chain B: T.432, S.434, S.437 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.432, B:S.434, B:S.437 NA.27: 4 residues within 4Å: Chain C: T.432, S.434, R.436, S.437 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.434, C:R.436, C:S.437 NA.36: 4 residues within 4Å: Chain D: I.124, K.125, G.126, T.129 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.127 NA.37: 4 residues within 4Å: Chain D: T.432, E.433, S.434, S.437 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.433, D:S.434, D:S.437 Water bridges: D:S.434

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: R.43, K.66, S.67, G.68, H.379 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.43, A:R.43 Water bridges: A:R.500 GOL.11: 9 residues within 4Å: Chain A: P.117, V.209, N.210, L.211, V.216, F.244, R.246, E.300 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.210, A:L.211, A:R.246, A:R.246 GOL.12: 8 residues within 4Å: Chain A: E.118, I.119, R.120, G.208, V.209, F.244, D.296 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.119, A:R.120, A:R.120 Water bridges: A:S.77 GOL.18: 4 residues within 4Å: Chain B: K.66, S.67, G.68, H.379 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.43, B:K.66 Water bridges: B:H.379 GOL.21: 9 residues within 4Å: Chain B: P.117, I.119, V.209, N.210, L.211, V.216, F.244, N.273, E.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.117, B:L.211, B:N.273 GOL.22: 6 residues within 4Å: Chain B: E.118, I.119, G.208, V.209, F.244, D.296 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.118, B:I.119, B:V.209, B:D.296 Water bridges: B:E.118, B:R.120 GOL.29: 6 residues within 4Å: Chain C: I.65, K.66, F.98, L.104, R.106, R.500 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.104, C:R.106, C:R.500, C:R.500 GOL.30: 6 residues within 4Å: Chain C: E.118, I.119, G.208, V.209, F.244, D.296 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.119, C:I.119, C:V.209 GOL.32: 6 residues within 4Å: Chain C: R.392, Y.421 Chain D: A.399, R.400, S.403, M.414 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Water bridges: D:A.399, D:S.403, D:S.403, D:S.403, C:E.418, C:Y.421, C:K.422 GOL.41: 7 residues within 4Å: Chain D: P.117, N.210, L.211, V.216, R.246, E.300 Ligands: GOL.42 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.117, D:L.211, D:R.246 GOL.42: 6 residues within 4Å: Chain D: E.118, I.119, V.209, F.244, D.296 Ligands: GOL.41 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.118, D:I.119, D:I.119

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

EDO.8: 3 residues within 4Å: Chain A: E.96, Y.105, H.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.105, A:Y.105, A:R.461 EDO.9: 6 residues within 4Å: Chain A: R.255, E.285, A.286, S.287, D.288, K.322 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.286, A:K.322 EDO.10: 6 residues within 4Å: Chain A: R.339, P.340, T.341, R.342 Chain C: D.178, Q.329 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.342, A:R.342, C:Q.329 EDO.19: 5 residues within 4Å: Chain B: A.38, P.39, I.40, T.41, R.383 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.41 EDO.20: 4 residues within 4Å: Chain B: D.178, D.296, I.299 Ligands: PYR.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.296 EDO.28: 4 residues within 4Å: Chain C: A.38, P.39, I.40, T.41 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.383 EDO.38: 3 residues within 4Å: Chain D: A.38, P.39, T.41 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.383 Water bridges: D:R.383 EDO.39: 6 residues within 4Å: Chain D: T.50, R.73, N.75, S.362, G.363, A.366 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.73, D:R.73, D:S.362 Water bridges: D:N.75, D:N.75, D:S.362, D:S.362 EDO.40: 4 residues within 4Å: Chain D: D.178, G.295, D.296 Ligands: PYR.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.178, D:D.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenton, A.W. et al., The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery. Protein Sci. (2010)

Release Date

2010-07-28

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase isozymes M1/M2

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