SMTL ID : 6v74.1

Crystal Structure of Human PKM2 in Complex with L-asparagine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: T.60, A.61, R.62, H.398 No protein-ligand interaction detected (PLIP) K.2: 6 residues within 4Å: Chain A: N.94, S.96, D.132, T.133, S.262, K.289 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.96, A:D.132, A:T.133 K.8: 6 residues within 4Å: Chain B: N.94, S.96, D.132, T.133, S.262, K.289 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.96, B:D.132, B:T.133 K.9: 4 residues within 4Å: Chain B: K.289, E.291, D.315 Ligands: OXL.21 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.291, B:D.315

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.69, R.92, N.94, S.381, G.382, A.385, K.386 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: P.136, I.138, V.228, N.229, L.230, F.263, R.265, E.319 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain B: T.69, R.92, N.94, S.381, G.382, A.385, K.386 Ligands: GOL.14 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: E.115, Y.124, P.476, R.480, L.492, K.494 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: T.347, Q.348, E.351, S.381, G.382, E.383 Ligands: GOL.12 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: R.418 Chain C: E.437, F.440, K.441 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: F.45 Chain B: L.372, Y.409, L.413 Ligands: GOL.17 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: K.330, N.369 Chain B: K.330, N.369, L.372, D.373 Ligands: GOL.16 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: D.388, Y.389, P.390, L.391, E.392 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain B: W.534, R.535 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: T.60, A.61, R.62, H.398 Ligands: ASN.11 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain B: W.534, N.542 Chain C: R.545, V.547 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain D: E.137, I.138, R.139, G.227, V.228, N.229, F.263, D.315 Ligands: MG.37 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain D: D.197, T.347, Q.348, E.351, S.381, G.382 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain A: R.418 Chain D: E.437, K.441 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain D: W.501, A.502, V.505, D.506, T.532, G.533 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain D: D.506, V.509, N.510, R.545, P.550 Ligand excluded by PLIP

4 x OXL: OXALATE ION(Non-covalent)

OXL.5: 9 residues within 4Å: Chain A: R.92, K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.314, A:D.315, A:T.347, A:T.347, A:T.347 Salt bridges: A:R.92, A:K.289, A:K.289 OXL.21: 9 residues within 4Å: Chain B: K.289, E.291, A.312, R.313, G.314, D.315, T.347, M.379 Ligands: K.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.291, B:E.291, B:E.291, B:G.314, B:D.315 Water bridges: B:R.92 Salt bridges: B:R.92, B:K.289, B:K.289 OXL.24: 9 residues within 4Å: Chain C: K.289, E.291, A.312, R.313, G.314, D.315, T.347, M.379 Ligands: MG.26 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.314, C:D.315, C:T.347, C:T.347 Salt bridges: C:R.92, C:K.289, C:K.289 OXL.35: 8 residues within 4Å: Chain D: K.289, E.291, A.312, R.313, G.314, D.315, T.347 Ligands: MG.37 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.314, D:D.315, D:T.347, D:T.347, D:T.347 Salt bridges: D:R.92, D:K.289

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

FBP.6: 16 residues within 4Å: Chain A: 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 18 PLIP interactions: 18 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:R.535, A:G.537, A:S.538, A:G.539, A:F.540 Water bridges: A:R.508, A:R.508 Salt bridges: A:K.452, A:R.508 FBP.22: 17 residues within 4Å: Chain B: L.450, T.451, K.452, S.453, R.455, S.456, W.501, R.508, G.533, W.534, 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: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 Water bridges: B:R.508 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 13 PLIP interactions: 13 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:G.533, C:G.533, C:G.537, C:S.538, C:G.539, C:F.540 Salt bridges: C:R.508 FBP.36: 18 residues within 4Å: Chain D: L.450, T.451, K.452, S.453, G.454, R.455, S.456, W.501, R.508, G.533, W.534, R.535, P.536, G.537, S.538, G.539, F.540, T.541 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.452, D:S.453, D:G.454, D:S.456, D:S.456, D:G.533, 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.7: 5 residues within 4Å: Chain A: F.263, K.289, E.291, D.315 Ligands: OXL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.291, A:D.315 MG.26: 3 residues within 4Å: Chain C: E.291, D.315 Ligands: OXL.24 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.315 MG.27: 4 residues within 4Å: Chain C: R.75, Y.102, E.105, T.106 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain D: E.291, D.315 Ligands: GOL.30, OXL.35 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.291, D:D.315

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

CL.10: 2 residues within 4Å: Chain B: P.72, R.75 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain D: T.69, R.92, N.94, S.381 Ligand excluded by PLIP

1 x ASN: ASPARAGINE(Non-covalent)

ASN.11: 16 residues within 4Å: Chain B: R.62, N.63, T.64, G.65, N.89, R.125, D.376, A.482, H.483, Y.485, R.486, G.487, I.488, F.489, P.490 Ligands: GOL.20 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.89, B:N.89, B:H.483, B:G.487, B:I.488, B:I.488, N.11 Salt bridges: B:R.62, B:R.125, B:H.483

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.28: 7 residues within 4Å: Chain C: F.45, K.330, N.369, L.372 Chain D: K.330, N.369, D.373 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.330, C:K.330 Salt bridges: D:D.373

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
A

B
C

C
D

D
B

Pyruvate kinase PKM

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