SMTL ID : 6v76.1

Crystal Structure of Human PKM2 in Complex with L-valine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.92, N.94, S.381 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain D: T.69, R.92, N.94, S.381 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.132, A:T.133

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.289, E.291, D.315 Ligands: OXL.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.291, A:D.315 MG.12: 4 residues within 4Å: Chain B: K.289, E.291, D.315 Ligands: OXL.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.291, B:D.315

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

FBP.4: 18 residues within 4Å: Chain A: L.450, T.451, K.452, S.453, G.454, R.455, S.456, W.501, R.508, T.532, G.533, R.535, P.536, G.537, S.538, G.539, F.540, T.541 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.451, A:K.452, A:S.453, A:G.454, A:R.455, A:S.456, A:S.456, A:S.456, A:G.533, A:G.533, A:G.537, A:S.538, A:G.539, A:F.540, A:T.541 Salt bridges: A:K.452, A:R.508 FBP.13: 16 residues within 4Å: Chain B: 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 14 PLIP interactions: 14 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:G.533, B:G.533, B:R.535, B:G.537, B:S.538, B:G.539, B:F.540 Salt bridges: B:R.508 FBP.18: 15 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:T.451, C:K.452, C:S.453, C:G.454, C:S.456, C:S.456, C:G.533, C:R.535, C:G.537, C:S.538, C:F.540, C:T.541 Salt bridges: C:R.508 FBP.23: 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 15 PLIP interactions: 15 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:G.533, D:G.533, D:R.535, D:G.537, D:G.539, D:F.540, D:T.541 Salt bridges: D:R.508

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: P.72, R.75, Y.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.72, A:R.75 GOL.6: 7 residues within 4Å: Chain A: P.136, V.228, N.229, L.230, V.235, F.263, E.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.136, A:N.229, A:L.230, A:E.319 GOL.7: 2 residues within 4Å: Chain A: E.272, K.275 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: D.300, R.335 Chain B: C.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.300, A:R.335 GOL.9: 6 residues within 4Å: Chain A: R.62, K.85, S.86, G.87, H.398 Ligands: VAL.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62, A:H.398 GOL.14: 5 residues within 4Å: Chain B: R.62, K.85, S.86, G.87, H.398 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.62 GOL.15: 2 residues within 4Å: Chain B: S.119, D.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.119 GOL.19: 2 residues within 4Å: Chain C: A.73, T.79 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.73 GOL.20: 7 residues within 4Å: Chain C: N.283, K.285, S.453, N.475, Q.477, T.478, Q.481 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.283, C:N.475, C:Q.477, C:Q.481 GOL.21: 4 residues within 4Å: Chain B: R.418 Chain C: E.437, F.440, K.441 No protein-ligand interaction detected (PLIP) GOL.24: 3 residues within 4Å: Chain C: F.45, Y.409 Chain D: F.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.409 GOL.25: 4 residues within 4Å: Chain D: Y.389, P.390, L.391, E.392 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.391

2 x OXL: OXALATE ION(Non-covalent)

OXL.10: 8 residues within 4Å: Chain A: K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.3 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 OXL.16: 9 residues within 4Å: Chain B: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.291, B:E.291, B:G.314, B:D.315, B:D.315 Salt bridges: B:R.92, B:K.289, B:K.289

2 x VAL: VALINE(Non-covalent)

VAL.11: 12 residues within 4Å: Chain A: R.62, N.63, T.64, G.65, N.89, R.125, H.483, Y.485, I.488, F.489, P.490 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain A, Hydrogen bonds: A:N.89, A:N.89, A:R.125, A:H.483 Salt bridges: A:R.62, A:R.125, A:H.483 VAL.17: 9 residues within 4Å: Chain B: R.62, N.63, G.65, N.89, R.125, H.483, I.488, F.489, P.490 7 PLIP interactions: 7 interactions with chain B, Hydrogen bonds: B:N.89, B:N.89, B:R.125, B:H.483 Salt bridges: B:R.62, B:R.125, B:H.483

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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