SMTL ID : 8hmu.1

Crystal Structure of PKM2 mutant R516C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

FBP.1: 8 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, G.455, R.456, S.457, T.542 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.452, A:K.453, A:S.454, A:G.455, A:R.456, A:S.457, A:S.457, A:S.457 FBP.10: 10 residues within 4Å: Chain B: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, T.542 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.452, B:K.453, B:S.454, B:G.455, B:R.456, B:S.457, B:S.457, B:T.542 Salt bridges: B:R.509 FBP.12: 4 residues within 4Å: Chain B: R.266, H.294, E.295, R.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.295 Salt bridges: B:R.266, B:H.294, B:R.298 FBP.19: 10 residues within 4Å: Chain C: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, T.542 10 PLIP interactions: 10 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, C:T.542 Salt bridges: C:R.509 FBP.29: 8 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, G.455, R.456, S.457, T.542 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.453, D:S.454, D:G.455, D:R.456, D:S.457, D:S.457, D:S.457

5 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.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.315, A:D.316, A:D.316 Water bridges: A:S.263 Salt bridges: A:R.93, A:K.290, A:K.290 OXL.6: 2 residues within 4Å: Chain A: H.98, G.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.99 Salt bridges: A:H.98, A:H.98 OXL.11: 8 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.17 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:D.316, B:T.348, B:T.348, B:T.348 Water bridges: B:K.290 Salt bridges: B:R.93, B:K.290, B:K.290 OXL.20: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.27 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.315, C:D.316, C:T.348 Water bridges: C:R.93 Salt bridges: C:R.93, C:K.290, C:K.290 OXL.30: 10 residues within 4Å: Chain D: R.93, K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348 Ligands: MG.35 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.315, D:D.316, D:T.348 Salt bridges: D:R.93, D:K.290, D:K.290

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

EDO.3: 8 residues within 4Å: Chain A: R.63, N.64, G.66, N.90, H.484, Y.486, I.489, F.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.484 EDO.4: 5 residues within 4Å: Chain A: P.137, N.230, L.231, V.236, E.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.229, A:N.230, A:L.231 EDO.7: 4 residues within 4Å: Chain A: N.95, S.97, H.98, R.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.95, A:S.97, A:S.97, A:R.140 Water bridges: A:K.387 EDO.13: 2 residues within 4Å: Chain B: H.98, G.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.99 EDO.14: 7 residues within 4Å: Chain B: P.137, V.229, N.230, L.231, V.236, F.264, E.320 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.137, B:N.230, B:L.231, B:E.320 EDO.23: 3 residues within 4Å: Chain C: H.98, R.140, K.226 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.140, C:K.226 EDO.31: 5 residues within 4Å: Chain D: K.250, L.278, G.279, E.280, K.281 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.280, D:K.281

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: E.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.295 GOL.24: 8 residues within 4Å: Chain C: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.64, C:H.484, C:I.489

10 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain A: R.456, H.459 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.456, A:H.459 PO4.15: 3 residues within 4Å: Chain B: N.95, H.98, R.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.95 Salt bridges: B:H.98, B:R.140 PO4.16: 2 residues within 4Å: Chain B: H.399, R.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.399 Salt bridges: B:R.403 PO4.21: 2 residues within 4Å: Chain C: T.100, H.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.101 Salt bridges: C:H.101 PO4.22: 3 residues within 4Å: Chain C: S.97, H.98, G.99 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.99 Salt bridges: C:H.98 PO4.25: 3 residues within 4Å: Chain C: H.294, E.295, R.298 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.298, C:R.298, C:R.298 Salt bridges: C:H.294, C:R.298 PO4.26: 2 residues within 4Å: Chain C: H.399, R.403 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.399, C:R.403 PO4.32: 2 residues within 4Å: Chain D: H.294, E.295 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.294 PO4.33: 4 residues within 4Å: Chain D: S.97, H.98, G.99, K.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.99 Salt bridges: D:H.98, D:K.226 PO4.34: 3 residues within 4Å: Chain D: N.95, H.98, R.140 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.95, D:R.140 Salt bridges: D:H.98

7 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: E.292, D.316 Ligands: OXL.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.292, A:D.316, H2O.2 MG.17: 3 residues within 4Å: Chain B: E.292, D.316 Ligands: OXL.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.18: 5 residues within 4Å: Chain B: N.95, S.97, D.133, T.134, S.263 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.97, B:D.133, B:T.134, H2O.4 MG.27: 5 residues within 4Å: Chain C: F.264, K.290, E.292, D.316 Ligands: OXL.20 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.28: 6 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263, K.290 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.97, C:D.133, C:T.134, H2O.8 MG.35: 4 residues within 4Å: Chain D: K.290, E.292, D.316 Ligands: OXL.30 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316 MG.36: 5 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, S.263 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.97, D:D.133, D:T.134

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
B

B
C

C
D

D
A

Pyruvate kinase PKM