SMTL ID : 3srf.3 (2 other biounits)

Human M1 pyruvate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: T.452, E.453, S.454, G.455, R.456, S.457, G.540 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.453, A:S.454, A:S.454, A:G.455, A:S.457, A:S.457 Water bridges: A:E.453 Salt bridges: A:R.456 PO4.6: 9 residues within 4Å: Chain B: L.451, T.452, E.453, S.454, G.455, R.456, S.457, G.540, F.541 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.452, B:T.452, B:E.453, B:S.454, B:G.455, B:S.457 Salt bridges: B:R.456 PO4.11: 7 residues within 4Å: Chain C: T.452, E.453, S.454, G.455, R.456, S.457, G.540 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.452, C:E.453, C:S.454, C:S.454, C:G.455, C:S.457, C:S.457 Salt bridges: C:R.456 PO4.16: 9 residues within 4Å: Chain D: L.451, T.452, E.453, S.454, G.455, R.456, S.457, G.540, F.541 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.452, D:T.452, D:T.452, D:E.453, D:S.454, D:G.455, D:S.457 Salt bridges: D:R.456

4 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: R.93, N.95, S.97, D.133, T.134, S.263, K.290 No protein-ligand interaction detected (PLIP) K.7: 7 residues within 4Å: Chain B: R.93, N.95, S.97, D.133, T.134, S.263, K.290 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.133 K.12: 7 residues within 4Å: Chain C: R.93, N.95, S.97, D.133, T.134, S.263, K.290 No protein-ligand interaction detected (PLIP) K.17: 7 residues within 4Å: Chain D: R.93, N.95, S.97, D.133, T.134, S.263, K.290 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.133

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.290, E.292, D.316 Ligands: PYR.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.292, A:D.316 MG.8: 3 residues within 4Å: Chain B: E.292, D.316 Ligands: PYR.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.13: 4 residues within 4Å: Chain C: K.290, E.292, D.316 Ligands: PYR.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.18: 3 residues within 4Å: Chain D: E.292, D.316 Ligands: PYR.19 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 10 residues within 4Å: Chain A: K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.290, A:G.315, A:D.316, A:T.348 Salt bridges: A:K.290 PYR.9: 10 residues within 4Å: Chain B: R.93, K.290, E.292, M.311, A.313, G.315, D.316, T.348, M.380 Ligands: MG.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.93, B:K.290, B:G.315, B:D.316, B:T.348 PYR.14: 10 residues within 4Å: Chain C: K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.290, C:E.292, C:G.315, C:D.316 Salt bridges: C:K.290 PYR.19: 10 residues within 4Å: Chain D: R.93, K.290, E.292, M.311, A.313, G.315, D.316, T.348, M.380 Ligands: MG.18 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.93, D:K.290, D:E.292, D:G.315, D:D.316

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490, P.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:H.484 GOL.10: 8 residues within 4Å: Chain B: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.63, B:R.63, B:H.484 Water bridges: B:R.63 GOL.15: 9 residues within 4Å: Chain C: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490, P.491 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.63, C:H.484, C:H.484 GOL.20: 8 residues within 4Å: Chain D: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.63, D:R.63, D:H.484 Water bridges: D:R.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgan, H.P. et al., Allosetric regulation of M2 pyruvate kinase. To be Published

Release Date

2012-08-08

Peptides

Pyruvate kinase isozymes M1/M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate kinase isozymes M1/M2

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