SMTL ID : 2g50.1 (1 other biounit)

The location of the allosteric amino acid binding site of muscle pyruvate kinase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: E.271, D.295 Ligands: PYR.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.271, A:D.295, H2O.11, H2O.11 MN.13: 3 residues within 4Å: Chain B: E.271, D.295 Ligands: PYR.17 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.271, B:D.295, H2O.42, H2O.42 MN.26: 3 residues within 4Å: Chain C: E.271, D.295 Ligands: PYR.30 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.271, C:D.295, H2O.53, H2O.53 MN.37: 3 residues within 4Å: Chain D: E.271, D.295 Ligands: PYR.42 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.271, D:D.295, H2O.90, H2O.91

4 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: N.74, S.76, D.112, T.113, S.242 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.76, A:D.112, A:T.113, H2O.11, H2O.11 K.14: 6 residues within 4Å: Chain B: N.74, S.76, D.112, T.113, S.242, K.269 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.76, B:D.112, B:T.113, H2O.42, H2O.42 K.27: 6 residues within 4Å: Chain C: N.74, S.76, D.112, T.113, S.242, K.269 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.76, C:D.112, C:T.113, H2O.53, H2O.53 K.38: 6 residues within 4Å: Chain D: N.74, S.76, D.112, T.113, S.242, K.269 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.76, D:D.112, D:T.113, H2O.90, H2O.91

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

NA.3: 5 residues within 4Å: Chain A: K.124, G.125, S.126, G.127, T.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.127 NA.4: 3 residues within 4Å: Chain A: T.431, S.433, S.436 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.431, A:T.431, A:S.436 Water bridges: A:E.432, A:E.432, A:S.433 NA.15: 3 residues within 4Å: Chain B: T.431, S.433, S.436 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.431, B:S.433, B:R.435, B:S.436 NA.28: 4 residues within 4Å: Chain C: T.431, S.433, R.435, S.436 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.433, C:R.435, C:S.436 NA.39: 5 residues within 4Å: Chain D: K.124, G.125, S.126, G.127, T.128 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.127 NA.40: 3 residues within 4Å: Chain D: T.431, S.433, S.436 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.431, D:R.435, D:S.436 Water bridges: D:E.432

4 x ALA: ALANINE(Non-covalent)

ALA.5: 8 residues within 4Å: Chain A: R.42, N.43, N.69, R.105, H.463, I.468, F.469, P.470 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.69, A:N.69, A:H.463 Water bridges: A:R.105 Salt bridges: A:R.42, A:R.105, A:H.463 ALA.16: 8 residues within 4Å: Chain B: R.42, N.43, N.69, H.463, I.468, F.469, P.470 Ligands: EDO.19 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.469 Hydrogen bonds: B:N.69, B:N.69, B:H.463 Water bridges: B:R.42 Salt bridges: B:H.463 ALA.29: 8 residues within 4Å: Chain C: R.42, N.43, N.69, R.105, H.463, I.468, F.469, P.470 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.69, C:N.69, C:H.463 Water bridges: C:R.105 Salt bridges: C:R.42, C:R.105, C:H.463 ALA.41: 8 residues within 4Å: Chain D: R.42, N.43, N.69, R.105, H.463, I.468, F.469, P.470 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.69, D:N.69, D:H.463 Water bridges: D:R.105 Salt bridges: D:R.42, D:R.105, D:H.463

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.6: 9 residues within 4Å: Chain A: K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.292 Hydrogen bonds: A:K.269, A:G.294, A:D.295 Water bridges: A:R.72 Salt bridges: A:K.269 PYR.17: 10 residues within 4Å: Chain B: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MN.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.269, B:E.271, B:G.294, B:D.295, B:D.295 Water bridges: B:R.72 Salt bridges: B:K.269 PYR.30: 10 residues within 4Å: Chain C: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MN.26 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.269, C:G.294, C:D.295 Water bridges: C:R.72 Salt bridges: C:K.269 PYR.42: 11 residues within 4Å: Chain D: R.72, K.269, E.271, M.290, A.292, R.293, G.294, D.295, T.327 Ligands: MN.37, EDO.45 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.269, D:G.294, D:D.295, D:T.327 Water bridges: D:R.72 Salt bridges: D:K.269

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

EDO.7: 4 residues within 4Å: Chain A: E.95, Y.104, H.456, R.460 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.104, A:Y.104, A:R.460 EDO.8: 6 residues within 4Å: Chain A: R.254, E.284, A.285, S.286, D.287, K.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.285, A:K.321 EDO.9: 7 residues within 4Å: Chain A: R.338, P.339, T.340, R.341 Chain C: D.177, L.179, Q.328 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.341, A:R.341, C:Q.328 Water bridges: A:K.336, A:P.339 EDO.18: 5 residues within 4Å: Chain B: A.37, P.38, I.39, T.40, R.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.40 Water bridges: B:R.382 EDO.19: 9 residues within 4Å: Chain B: N.69, Y.104, R.105, P.106, H.463, F.469, P.470, R.499 Ligands: ALA.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.69, B:P.470, B:R.499, B:R.499, A.16 EDO.20: 6 residues within 4Å: Chain B: R.254, E.284, A.285, S.286, D.287, K.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.321, B:K.321 EDO.21: 6 residues within 4Å: Chain B: D.177, G.294, D.295, I.298, T.327 Ligands: GOL.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.177, B:D.295 Water bridges: B:Q.328 EDO.31: 5 residues within 4Å: Chain C: A.37, P.38, I.39, T.40, R.382 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.40, C:R.382 EDO.32: 5 residues within 4Å: Chain A: D.177, Q.328 Chain C: R.338, P.339, R.341 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:D.177, A:D.177, A:Q.328, C:P.339, C:R.341 Water bridges: C:R.341, C:R.341 EDO.43: 4 residues within 4Å: Chain D: A.37, P.38, I.39, T.40 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.40, D:R.382 Water bridges: D:R.382, D:R.382 EDO.44: 5 residues within 4Å: Chain D: T.49, R.72, N.74, S.361, G.362 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.72, D:R.72 Water bridges: D:N.74, D:N.74, D:N.74, D:S.361, D:S.361 EDO.45: 5 residues within 4Å: Chain D: D.177, G.294, D.295, I.298 Ligands: PYR.42 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.294 EDO.46: 3 residues within 4Å: Chain D: T.138, E.153, N.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.138, D:T.138 Water bridges: D:T.138

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain A: P.116, V.208, N.209, L.210, V.215, R.245, E.299 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.116, A:L.210, A:R.245, A:E.299 GOL.11: 7 residues within 4Å: Chain A: E.117, I.118, G.207, V.208, F.243, D.295 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.117, A:I.118, A:R.119 Water bridges: A:S.76 GOL.12: 5 residues within 4Å: Chain A: R.42, K.65, S.66, G.67, H.378 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.42 Water bridges: A:R.42, A:R.42, A:H.378, A:R.499, A:R.499, A:R.499, A:R.499 GOL.23: 8 residues within 4Å: Chain B: P.116, V.208, N.209, L.210, V.215, R.245, E.299 Ligands: GOL.24 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.116, B:L.210, B:R.245, B:E.299 Water bridges: B:L.217, B:R.245 GOL.24: 8 residues within 4Å: Chain B: E.117, I.118, G.207, V.208, F.243, D.295 Ligands: EDO.21, GOL.23 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.117, B:I.118, B:R.119, B:R.119, B:V.208, B:D.295 GOL.25: 5 residues within 4Å: Chain B: R.42, K.65, S.66, G.67, H.378 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.42 Water bridges: B:R.42, B:R.42, B:H.378 GOL.33: 8 residues within 4Å: Chain C: P.116, V.208, N.209, L.210, V.215, R.245, E.299 Ligands: GOL.34 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:P.116, C:L.210, C:R.245, C:R.245, C:E.299 Water bridges: C:V.215, C:L.217 GOL.34: 8 residues within 4Å: Chain C: E.117, I.118, R.119, G.207, V.208, F.243, D.295 Ligands: GOL.33 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.118, C:I.118, C:V.208, C:D.295 GOL.35: 6 residues within 4Å: Chain C: I.64, F.97, L.103, Y.104, R.105, R.499 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.105, C:R.105, C:R.499, C:R.499 Water bridges: C:K.65, C:F.97, C:L.103 GOL.36: 6 residues within 4Å: Chain C: E.417, Y.420, K.421 Chain D: A.398, S.402, M.413 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Water bridges: D:S.402, C:R.391, C:E.395, C:Y.420 GOL.47: 8 residues within 4Å: Chain D: P.116, V.208, N.209, L.210, V.215, R.245, E.299 Ligands: GOL.48 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:P.116, D:L.210, D:R.245, D:E.299 Water bridges: D:V.215, D:N.272 GOL.48: 8 residues within 4Å: Chain D: E.117, I.118, R.119, G.207, V.208, F.243, D.295 Ligands: GOL.47 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.117, D:I.118, D:I.118, D:R.119, D:V.208, D:D.295 Water bridges: D:S.76

1 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.22: 9 residues within 4Å: Chain B: T.49, I.50, G.51, P.52, R.72, N.74, S.361, A.365, K.366 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.72, B:R.72, B:N.74 Water bridges: B:S.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, R. et al., Differentiating a Ligand's Chemical Requirements for Allosteric Interactions from Those for Protein Binding. Phenylalanine Inhibition of Pyruvate Kinase. Biochemistry (2006)

Release Date

2006-05-09

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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