SMTL ID : 8f6m.1 (1 other biounit)

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: T.50, P.53, R.73, N.75, H.78, Y.83, H.84, R.120, K.207, S.362, G.363, A.366, K.367 Ligands: SIN.2, MN.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.75, A:H.84, A:K.207, A:K.207, A:S.362 Water bridges: A:H.78, A:R.120, A:R.120, A:E.131, A:D.177, A:D.177, A:D.177, A:G.363 Salt bridges: A:R.73, A:H.78, A:R.120 pi-Stacking: A:H.78, A:H.78 ADP.12: 13 residues within 4Å: Chain B: P.53, R.73, N.75, H.78, Y.83, H.84, R.120, S.362, G.363, A.366, K.367 Ligands: GZ3.13, MN.14 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.75, B:Y.83, B:H.84 Water bridges: B:H.84, B:R.120, B:K.207, B:K.207, B:S.362, B:S.362 Salt bridges: B:R.73, B:H.78, B:R.120 pi-Cation interactions: B:H.78, B:H.78

5 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 13 residues within 4Å: Chain A: R.73, K.270, E.272, M.291, A.293, G.295, D.296, T.328, M.360, S.362 Ligands: ADP.1, MN.3, MN.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.293 Hydrogen bonds: A:G.295, A:D.296, A:S.362 Water bridges: A:R.73, A:N.75, A:K.270 Salt bridges: A:R.73, A:K.270 SIN.6: 7 residues within 4Å: Chain A: T.432, E.433, S.434, R.436, S.437, G.520, F.521 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.433, A:S.434, A:S.434, A:S.437, A:G.520 Salt bridges: A:R.436 SIN.17: 7 residues within 4Å: Chain B: T.432, E.433, S.434, R.436, S.437, G.520, F.521 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.433, B:S.434, B:S.434, B:R.436, B:S.437, B:S.437, B:G.520 Salt bridges: B:R.436 SIN.27: 7 residues within 4Å: Chain C: T.432, E.433, S.434, R.436, S.437, G.520, F.521 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:R.436 Hydrogen bonds: C:T.432, C:E.433, C:S.434, C:S.434, C:S.437, C:S.437 SIN.34: 7 residues within 4Å: Chain D: T.432, E.433, S.434, R.436, S.437, G.520, F.521 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.432, D:E.433, D:S.434, D:S.434, D:R.436, D:S.437, D:G.520 Salt bridges: D:R.436

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

MN.3: 3 residues within 4Å: Chain A: D.178 Ligands: ADP.1, SIN.2 No protein-ligand interaction detected (PLIP) MN.4: 3 residues within 4Å: Chain A: E.272, D.296 Ligands: SIN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.272, A:D.296, H2O.2, H2O.3 MN.14: 3 residues within 4Å: Chain B: D.178 Ligands: ADP.12, GZ3.13 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.178, H2O.17 MN.15: 3 residues within 4Å: Chain B: E.272, D.296 Ligands: GZ3.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.272, B:D.296, H2O.17 MN.25: 4 residues within 4Å: Chain C: F.244, E.272, D.296 Ligands: GZ3.24 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.272, C:D.296, H2O.31 MN.32: 3 residues within 4Å: Chain D: E.272, D.296 Ligands: GZ3.31 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.272, D:D.296, H2O.44, H2O.52, H2O.53 MN.38: 3 residues within 4Å: Chain D: G.295, D.296 Ligands: GZ3.31 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.296, H2O.54, H2O.55, H2O.56

4 x K: POTASSIUM ION(Non-covalent)

K.5: 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.2 K.16: 7 residues within 4Å: Chain B: N.75, S.77, D.113, T.114, S.243, K.270 Ligands: GZ3.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.77, B:D.113, B:T.114, H2O.20 K.26: 7 residues within 4Å: Chain C: N.75, S.77, D.113, T.114, S.243, K.270 Ligands: GZ3.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.77, C:D.113, C:T.114, H2O.35 K.33: 6 residues within 4Å: Chain D: N.75, S.77, D.113, T.114, K.270 Ligands: GZ3.31 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.77, D:D.113, D:T.114, H2O.43, H2O.51

4 x ALA: ALANINE(Non-covalent)

ALA.7: 8 residues within 4Å: Chain A: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: A.7, A:N.70, A:H.464, A:I.469 Water bridges: A:R.106, A:R.106 Salt bridges: A:R.43, A:R.106, A:H.464 ALA.18: 8 residues within 4Å: Chain B: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.70, B:N.70, B:H.464 Water bridges: B:N.44, B:R.106, B:I.469 Salt bridges: B:R.43, B:R.106, B:H.464 ALA.28: 8 residues within 4Å: Chain C: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.70, C:N.70, C:H.464 Water bridges: C:N.44, C:R.106, C:R.106, C:I.469 Salt bridges: C:R.43, C:R.106, C:H.464 ALA.35: 8 residues within 4Å: Chain D: R.43, N.44, N.70, R.106, H.464, I.469, F.470, P.471 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain D Hydrogen bonds: A.35, D:N.70, D:H.464, D:I.469 Water bridges: D:R.106 Salt bridges: D:R.106, D:H.464

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: D.178, G.179, L.180, Q.329 Chain C: K.337, R.339, P.340, T.341, R.342 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.342, C:R.342, A:D.178, A:G.179, A:Q.329 Water bridges: C:R.339 GOL.9: 7 residues within 4Å: Chain A: R.392, Y.421, K.422 Chain B: A.399, R.400, S.403 Ligands: GOL.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.392, A:R.392, A:Y.421, B:S.403 GOL.10: 7 residues within 4Å: Chain A: R.392, E.396, E.418, Y.421 Chain B: E.396 Ligands: GOL.9, GOL.21 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.392, B:E.396 GOL.11: 5 residues within 4Å: Chain A: P.302, A.303, E.304 Chain C: R.339, M.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.303, A:E.304 GOL.19: 7 residues within 4Å: Chain A: A.399, R.400, S.403 Chain B: R.392, Y.421, K.422 Ligands: GOL.21 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.399, B:R.392, B:R.392 Water bridges: A:S.403, A:S.405 GOL.20: 4 residues within 4Å: Chain B: F.26, M.30 Chain D: F.26 Ligands: GOL.23 No protein-ligand interaction detected (PLIP) GOL.21: 8 residues within 4Å: Chain A: F.395 Chain B: R.392, F.395, E.396, E.418, Y.421 Ligands: GOL.10, GOL.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.396, A:E.418 Water bridges: B:E.396 GOL.22: 6 residues within 4Å: Chain B: D.407, M.409, E.410, R.436, Q.440, R.443 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.410, B:R.436, B:R.436, B:R.443, B:R.443 Water bridges: B:A.320, B:S.405, B:Q.440 GOL.23: 9 residues within 4Å: Chain B: F.26, L.27, M.30 Chain D: F.26, L.353, D.354, L.394, E.397 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.354 GOL.29: 5 residues within 4Å: Chain C: R.392, K.422 Chain D: A.399, R.400, S.403 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Water bridges: C:Y.421, C:Y.421, C:R.447, D:R.400, D:S.405 Hydrogen bonds: D:A.399 GOL.30: 5 residues within 4Å: Chain C: D.407, E.410, R.436, Q.440, R.443 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.407, C:R.436, C:R.443, C:R.443 Water bridges: C:A.320, C:S.405, C:Q.440 GOL.36: 3 residues within 4Å: Chain D: E.59, T.60, E.63 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.60 GOL.37: 5 residues within 4Å: Chain D: D.407, E.410, R.436, Q.440, R.443 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.410, D:E.410, D:R.436, D:R.443, D:R.443 Water bridges: D:S.405, D:D.407, D:Q.440

3 x GZ3: (E)-2-METHYL-3-PHOSPHONOACRYLATE(Non-covalent)

GZ3.13: 14 residues within 4Å: Chain B: R.73, N.75, D.113, K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: ADP.12, MN.14, MN.15, K.16 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.73, B:N.75, B:N.75, B:S.77, B:D.113, B:K.270, B:G.295, B:D.296, B:T.328, B:T.328 Water bridges: B:E.118, B:E.118 GZ3.24: 12 residues within 4Å: Chain C: R.73, N.75, D.113, K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MN.25, K.26 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.293 Hydrogen bonds: C:R.73, C:N.75, C:K.270, C:G.295, C:D.296, C:T.328, C:T.328 Water bridges: C:E.118 GZ3.31: 11 residues within 4Å: Chain D: R.73, K.270, E.272, A.293, R.294, G.295, D.296, T.328 Ligands: MN.32, K.33, MN.38 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.293 Hydrogen bonds: D:R.73, D:K.270, D:G.295, D:D.296, D:D.296, D:D.296 Water bridges: D:S.77, D:S.77

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
F

C
G

D
H

Pyruvate kinase PKM

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