SMTL ID : 6gg4.1

Crystal structure of M2 PYK in complex with Phenyalanine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: T.452, K.453, S.454, G.455, R.456, S.457 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:G.455, A:S.457, A:S.457 Water bridges: A:K.453, A:G.540 Salt bridges: A:K.453 PO4.2: 3 residues within 4Å: Chain A: N.95, H.98, R.140 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95 Water bridges: A:R.140, A:R.140, A:R.140 Salt bridges: A:H.98, A:R.140 PO4.4: 4 residues within 4Å: Chain A: S.97, H.98, G.99, K.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.97, A:G.99 Water bridges: A:H.98 Salt bridges: A:H.98, A:K.226 PO4.6: 5 residues within 4Å: Chain B: T.452, K.453, S.454, R.456, S.457 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.453, B:S.454, B:S.454, B:G.455, B:S.457, B:S.457 Water bridges: B:L.451, B:K.453 Salt bridges: B:K.453 PO4.7: 4 residues within 4Å: Chain B: N.95, H.98, R.140, D.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.95 Salt bridges: B:H.98, B:R.140 PO4.9: 4 residues within 4Å: Chain B: S.97, H.98, G.99, K.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.99 Salt bridges: B:H.98, B:K.226 PO4.11: 6 residues within 4Å: Chain C: T.452, K.453, S.454, G.455, R.456, S.457 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:S.454, C:G.455, C:S.457, C:S.457 Water bridges: C:K.453, C:K.453, C:G.540 Salt bridges: C:K.453 PO4.14: 6 residues within 4Å: Chain D: T.452, K.453, S.454, G.455, R.456, S.457 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.453, D:S.454, D:G.455, D:S.457 Salt bridges: D:K.453

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.3: 11 residues within 4Å: Chain A: R.63, N.64, T.65, N.90, R.126, H.484, G.488, I.489, F.490, P.491, F.522 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:F.490, A:F.490, A:F.522 Hydrogen bonds: A:N.90, A:N.90, A:H.484 Water bridges: A:N.64, A:I.489 Salt bridges: A:R.63, A:R.126, A:H.484 PHE.8: 10 residues within 4Å: Chain B: R.63, N.64, T.65, N.90, R.126, H.484, G.488, I.489, F.490, P.491 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.490, B:F.490 Hydrogen bonds: B:N.90, B:H.484, B:I.489, F.8 Salt bridges: B:R.126, B:H.484 PHE.12: 10 residues within 4Å: Chain C: R.63, N.64, T.65, N.90, R.126, H.484, G.488, I.489, F.490, P.491 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:F.490, C:F.490 Hydrogen bonds: C:N.90 Water bridges: C:N.64, C:R.126, C:I.489 Salt bridges: C:R.126, C:H.484 PHE.15: 11 residues within 4Å: Chain D: R.63, N.64, T.65, N.90, R.126, H.484, G.488, I.489, F.490, P.491, F.522 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.490, D:F.490, D:F.522 Hydrogen bonds: D:R.63, D:N.90, D:H.484, F.15, F.15 Salt bridges: D:R.126, D:H.484

4 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.97, A:T.134, H2O.1, H2O.3 K.10: 5 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, S.263 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.97, B:T.134, H2O.5 K.13: 5 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.97, C:T.134 K.16: 5 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, S.263 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.133, D:T.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, M. et al., An allostatic mechanism for M2 pyruvate kinase as an amino-acid sensor. Biochem. J. (2018)

Release Date

2018-05-23

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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