SMTL ID : 6gg6.2 (1 other biounit)

Crystal structure of M2 PYK in complex with Serine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, E.138, S.263 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.97, A:D.133, A:T.134 K.5: 6 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, E.138, S.263 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.97, B:D.133 K.9: 6 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, E.138, S.263 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.97, C:D.133 K.13: 6 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, E.138, S.263 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.97, D:D.133

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.290, E.292, A.313, D.316, T.348 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: K.290, E.292, D.316 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.10: 3 residues within 4Å: Chain C: K.290, E.292, D.316 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.14: 4 residues within 4Å: Chain D: K.290, E.292, A.313, D.316 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316

4 x SER: SERINE(Non-covalent)

SER.3: 9 residues within 4Å: Chain A: R.63, N.64, G.66, N.90, R.126, H.484, I.489, F.490, P.491 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.90, A:N.90, A:I.489 Salt bridges: A:R.63, A:R.126, A:H.484 SER.7: 8 residues within 4Å: Chain B: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.90, B:H.484 Salt bridges: B:R.63, B:R.126, B:H.484 SER.11: 8 residues within 4Å: Chain C: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.90, C:H.484, C:H.484 Salt bridges: C:R.63, C:R.126, C:H.484 SER.15: 9 residues within 4Å: Chain D: R.63, N.64, G.66, N.90, R.126, H.484, I.489, F.490, P.491 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:N.90, D:N.90, D:I.489, S.15 Salt bridges: D:R.63, D:R.126, D:H.484

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

PO4.4: 9 residues within 4Å: Chain A: T.452, K.453, S.454, G.455, R.456, S.457, S.539, G.540, T.542 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.452, A:T.452, A:T.452, A:K.453, A:S.454, A:G.455, A:R.456, A:S.457, A:S.457, A:G.540, A:T.542 PO4.8: 10 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, G.455, R.456, S.457, S.539, G.540, T.542 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.453, B:S.454, B:G.455, B:R.456, B:S.457, B:S.457, B:S.457, B:G.540, B:T.542 PO4.12: 9 residues within 4Å: Chain C: T.452, K.453, S.454, G.455, R.456, S.457, S.539, G.540, T.542 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.452, C:T.452, C:K.453, C:S.454, C:G.455, C:R.456, C:S.457, C:G.540, C:T.542 PO4.16: 9 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, R.456, S.457, S.539, G.540, T.542 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.452, D:T.452, D:K.453, D:S.454, D:R.456, D:S.457, D:S.457, D:S.457, D:G.540

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
E

B
F

C
G

D
H

Pyruvate kinase PKM

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