SMTL ID : 8hms.1

Crystal Structure of PKM2 mutant C474S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 16 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:S.457, A:S.457, A:G.534, A:G.538, A:S.539, A:G.540, A:F.541, A:F.541 Water bridges: A:R.475, A:D.505, A:R.509, A:R.509 Salt bridges: A:K.453, A:R.509 FBP.9: 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:R.536, B:G.538, B:G.540, B:F.541 Salt bridges: B:R.509 FBP.14: 17 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:S.457, C:S.457, C:S.457, C:G.534, C:G.538, C:S.539, C:G.540, C:F.541, C:F.541 Water bridges: C:T.452, C:R.509 Salt bridges: C:R.509

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.315, A:D.316, A:D.316 Water bridges: A:R.93, A:K.290, A:E.292, A:D.316 Salt bridges: A:R.93, A:K.290 OXL.8: 9 residues within 4Å: Chain B: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:D.316, B:D.316 Water bridges: B:K.290 Salt bridges: B:R.93, B:K.290, B:K.290 OXL.13: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.18 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.292, C:G.315, C:D.316, C:T.348, C:T.348 Water bridges: C:R.93, C:K.290 Salt bridges: C:R.93, C:K.290 OXL.19: 9 residues within 4Å: Chain D: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.22 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.315, D:D.316, D:T.348, D:T.348 Water bridges: D:K.290 Salt bridges: D:R.93, D:K.290

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

EDO.3: 8 residues within 4Å: Chain A: R.63, N.64, T.65, G.66, N.90, H.484, Y.486, I.489 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.484 EDO.4: 7 residues within 4Å: Chain A: P.137, E.138, I.139, V.229, N.230, F.264, D.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.137, A:I.139, A:D.316 EDO.5: 5 residues within 4Å: Chain A: E.305, A.306, S.307, D.308, K.342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.306, A:K.342 EDO.10: 8 residues within 4Å: Chain B: N.64, G.66, N.90, A.483, H.484, Y.486, G.488, I.489 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.90, B:Y.486, B:G.488, B:I.489 EDO.11: 5 residues within 4Å: Chain B: V.229, N.230, L.231, F.264, E.320 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.231, B:L.231 EDO.15: 8 residues within 4Å: Chain B: R.359, P.360, T.361, R.362 Chain C: D.198, G.199, L.200, Q.349 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.360 Water bridges: B:R.362 EDO.20: 8 residues within 4Å: Chain D: P.137, I.139, V.229, N.230, L.231, F.264, R.266, E.320 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:P.137, D:N.230, D:L.231, D:R.266

5 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.2, H2O.2 MG.7: 5 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, S.263 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.133, A:T.134 MG.12: 4 residues within 4Å: Chain B: E.138, E.292, D.316 Ligands: OXL.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.292, B:D.316, H2O.5, H2O.6 MG.18: 4 residues within 4Å: Chain C: E.138, E.292, D.316 Ligands: OXL.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.292, C:D.316, H2O.9, H2O.9 MG.22: 3 residues within 4Å: Chain D: E.292, D.316 Ligands: OXL.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.292, D:D.316, H2O.14, H2O.15

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 7 residues within 4Å: Chain C: P.137, V.229, N.230, L.231, V.236, F.264, E.320 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:P.137, C:L.231, C:L.231 Water bridges: C:E.320, C:E.320 GOL.17: 10 residues within 4Å: Chain C: R.63, N.64, G.66, N.90, A.483, H.484, Y.486, G.488, I.489, F.490 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.64, C:N.90, C:N.90, C:A.483, C:H.484, C:I.489 GOL.21: 8 residues within 4Å: Chain D: R.63, N.64, G.66, N.90, H.484, Y.486, G.488, I.489 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.63, D:N.90, D:N.90, D:H.484, D:Y.486, D:G.488

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