SMTL ID : 6v75.1

Crystal Structure of Human PKM2 in Complex with L-aspartate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, K.289 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.133 K.2: 2 residues within 4Å: Chain A: L.123, R.125 No protein-ligand interaction detected (PLIP) K.11: 4 residues within 4Å: Chain B: N.94, S.96, D.132, T.133 No protein-ligand interaction detected (PLIP) K.21: 5 residues within 4Å: Chain C: N.94, S.96, D.132, T.133, E.137 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.96, C:D.132 K.22: 1 residues within 4Å: Chain C: D.506 No protein-ligand interaction detected (PLIP) K.27: 7 residues within 4Å: Chain D: N.94, S.96, D.132, T.133, K.134, E.137, S.262 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.96, D:T.133

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: E.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.272 GOL.4: 8 residues within 4Å: Chain A: P.136, I.138, N.229, L.230, V.235, L.237, F.263, E.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.230, A:E.319 GOL.5: 4 residues within 4Å: Chain A: Y.389, P.390, L.391, E.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.391, A:E.392 GOL.12: 5 residues within 4Å: Chain B: A.61, R.62, R.125, H.398 Ligands: ASP.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.62, B:R.125 GOL.13: 4 residues within 4Å: Chain A: F.45, D.373 Chain B: K.330, N.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.373 GOL.14: 6 residues within 4Å: Chain B: P.136, V.228, N.229, L.230, F.263, E.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.136, B:L.230 GOL.15: 4 residues within 4Å: Chain B: W.501, T.532, G.533, R.545 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.533, B:R.545 GOL.16: 5 residues within 4Å: Chain B: D.197, Q.348, E.351, S.381, G.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.348, B:E.351, B:S.381, B:G.382 GOL.23: 8 residues within 4Å: Chain C: N.63, T.64, V.371, G.374, A.375, I.408, R.464, R.486 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.63, C:V.371 GOL.24: 3 residues within 4Å: Chain B: R.418 Chain C: E.437, F.440 No protein-ligand interaction detected (PLIP) GOL.28: 2 residues within 4Å: Chain D: K.355, K.386 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.355, D:K.355 GOL.29: 4 residues within 4Å: Chain A: R.418, A.421 Chain D: E.437, K.441 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.418, A:A.421, D:E.437

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: T.69, R.92, N.94 Ligand excluded by PLIP

4 x FBP: 1,6-di-O-phosphono-beta-D-fructofuranose(Post Translational Modification)(Non-covalent)

FBP.7: 15 residues within 4Å: Chain A: L.450, T.451, K.452, S.453, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:S.456, A:S.456, A:R.508, A:G.533, A:R.535, A:G.537, A:G.539, A:F.540 Salt bridges: A:K.452, A:R.508 FBP.17: 16 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, S.456, W.501, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.451, B:K.452, B:S.453, B:G.454, B:S.456, B:S.456, B:R.508, B:T.532, B:G.533, B:G.537, B:G.539, B:F.540, B:F.540, B:T.541, B:T.541 Salt bridges: B:R.508 FBP.25: 17 residues within 4Å: Chain C: L.450, T.451, K.452, S.453, G.454, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:R.455, C:S.456, C:R.535, C:G.537, C:S.538, C:G.539, C:F.540 Salt bridges: C:R.508 FBP.30: 16 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:K.452, D:S.453, D:G.454, D:R.455, D:S.456, D:S.456, D:S.456, D:R.474, D:D.504, D:D.504, D:R.535, D:G.537, D:S.538, D:G.539, D:F.540 Salt bridges: D:R.508

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: K.289, E.291, D.315 Ligands: OXL.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.291, A:D.315 MG.19: 2 residues within 4Å: Chain B: E.291, D.315 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.315 MG.26: 2 residues within 4Å: Chain C: E.291, D.315 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.291 MG.33: 3 residues within 4Å: Chain D: E.291, A.312, D.315 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.291, D:D.315

1 x OXL: OXALATE ION(Non-covalent)

OXL.9: 9 residues within 4Å: Chain A: K.289, E.291, M.310, A.312, R.313, G.314, D.315, T.347 Ligands: MG.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.314, A:D.315, A:T.347, A:T.347 Salt bridges: A:R.92, A:K.289, A:K.289

2 x ASP: ASPARTIC ACID(Non-covalent)

ASP.10: 10 residues within 4Å: Chain A: R.62, N.63, G.65, N.89, A.482, H.483, Y.485, R.486, G.487, I.488 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.65, A:N.89, A:N.89, A:H.483, A:H.483, A:G.487, A:I.488, D.10 Salt bridges: A:R.62 ASP.20: 15 residues within 4Å: Chain B: R.62, N.63, T.64, G.65, N.89, R.125, A.482, H.483, Y.485, R.486, G.487, I.488, F.489, P.490 Ligands: GOL.12 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.63, B:G.65, B:N.89, B:N.89, B:H.483, B:G.487, B:I.488, D.20 Salt bridges: B:R.62, B:R.125, B:H.483

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 2 residues within 4Å: Chain B: A.73, S.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.76 PEG.31: 4 residues within 4Å: Chain D: E.499, A.500, W.501, A.502 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.501 PEG.32: 2 residues within 4Å: Chain D: D.506, N.510 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.506

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nandi, S. et al., Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2. J.Biol.Chem. (2020)

Release Date

2020-03-18

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
D

D
A

Pyruvate kinase PKM

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