SMTL ID : 8hmq.1

Crystal Structure of PKM2 mutant P403A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x OXL: OXALATE ION(Non-covalent)

OXL.1: 8 residues within 4Å: Chain A: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.315, A:D.316, A:T.348, A:T.348, A:T.348 Water bridges: A:S.263 Salt bridges: A:R.93, A:K.290 OXL.10: 9 residues within 4Å: Chain B: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:D.316 Salt bridges: B:R.93, B:K.290 OXL.17: 10 residues within 4Å: Chain C: R.93, K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348 Ligands: MG.21 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.315, C:D.316, C:T.348, C:T.348 Salt bridges: C:R.93, C:K.290 OXL.22: 10 residues within 4Å: Chain D: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.27 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.292, D:G.315, D:D.316 Water bridges: D:R.93, D:R.93, D:S.263 Salt bridges: D:R.93, D:K.290, D:K.290

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.137, V.229, N.230, L.231, V.236, F.264, E.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.137, A:L.231, A:L.231, A:E.320 GOL.3: 8 residues within 4Å: Chain A: R.63, N.64, N.90, R.126, H.484, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.63, A:N.90, A:R.126, A:H.484, A:H.484 GOL.12: 7 residues within 4Å: Chain B: P.137, V.229, N.230, L.231, F.264, R.266, E.320 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.137, B:L.231, B:R.266, B:R.266, B:E.320 GOL.13: 10 residues within 4Å: Chain B: R.63, N.64, G.66, N.90, R.126, H.484, Y.486, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.64, B:N.90, B:R.126, B:H.484 Water bridges: B:R.126 GOL.19: 9 residues within 4Å: Chain C: R.63, N.64, G.66, N.90, R.126, H.484, I.489, F.490, P.491 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.64, C:N.90, C:R.126, C:H.484, C:H.484 GOL.24: 8 residues within 4Å: Chain D: R.63, N.64, G.66, N.90, R.126, H.484, I.489, F.490 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.64, D:N.90, D:R.126, D:H.484 Water bridges: D:R.126 GOL.26: 9 residues within 4Å: Chain A: R.420 Chain C: Q.413, E.417 Chain D: D.44, T.45, F.46, Y.410, Q.413, E.416 7 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:F.46, D:Y.410, D:E.416, C:Q.413, C:E.417, A:R.420 Water bridges: C:R.420

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: D.256, Q.478, R.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.481 EDO.5: 5 residues within 4Å: Chain A: R.63, K.86, S.87, G.88, H.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.63 EDO.6: 2 residues within 4Å: Chain A: N.515, K.518 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.518 EDO.20: 4 residues within 4Å: Chain C: R.359, P.360, R.362 Chain D: Q.349 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.349, C:R.359, C:R.362, C:R.362 EDO.25: 6 residues within 4Å: Chain D: P.137, V.229, N.230, L.231, V.236, E.320 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.231

9 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.1, H2O.1 MG.8: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263, K.290 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:S.97, A:D.133, A:T.134 MG.9: 5 residues within 4Å: Chain A: D.256, V.257, D.258, Q.478, R.481 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.256, A:D.258 MG.14: 5 residues within 4Å: Chain B: F.264, K.290, E.292, D.316 Ligands: OXL.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.292, B:E.292, B:D.316 MG.15: 7 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, E.138, S.263, K.290 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.97, B:D.133, B:T.134 MG.16: 7 residues within 4Å: Chain B: F.264, I.265, K.290, I.291, E.292, N.293, G.296 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.265 MG.21: 3 residues within 4Å: Chain C: E.292, D.316 Ligands: OXL.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.292, C:D.316, H2O.4 MG.27: 4 residues within 4Å: Chain D: K.290, E.292, D.316 Ligands: OXL.22 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.292, D:D.316, H2O.4 MG.28: 7 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, E.138, S.263, K.290 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.133, H2O.4

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

FBP.11: 17 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, T.533, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.452, B:K.453, B:S.454, B:G.455, B:S.457, B:S.457, B:G.534, B:G.538, B:S.539, B:G.540, B:F.541 Salt bridges: B:R.509 FBP.18: 7 residues within 4Å: Chain C: T.452, K.453, S.454, G.455, R.456, S.457, F.541 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:G.455, C:R.456, C:S.457, C:S.457, C:S.457 FBP.23: 11 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, G.455, R.456, S.457, G.538, S.539, G.540, T.542 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.452, D:K.453, D:S.454, D:G.455, D:S.457, D:S.457, D:S.457, D:G.540, D:T.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Upadhyay, S. et al., Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2. To Be Published

Release Date

2023-01-11

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM