SMTL ID : 8hmr.1

Crystal Structure of PKM2 mutant L144P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.292, A:G.315, A:D.316 Salt bridges: A:K.290 OXL.5: 8 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.292, B:G.315, B:D.316, B:D.316, B:T.348, B:T.348 Salt bridges: B:K.290 OXL.7: 10 residues within 4Å: Chain C: R.93, K.290, E.292, A.313, R.314, G.315, D.316, T.348, M.380 Ligands: MG.11 7 PLIP interactions: 7 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, C:K.290 OXL.13: 8 residues within 4Å: Chain D: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.292, D:G.315, D:D.316 Salt bridges: D:R.93, D:K.290

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

FBP.2: 17 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, R.456, S.457, W.502, R.509, G.534, W.535, R.536, P.537, G.538, S.539, G.540, F.541, T.542 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.453, A:S.454, A:S.454, A:S.454, A:S.457, A:S.457, A:G.534, A:R.536, A:G.538, A:G.538, A:S.539, A:G.540, A:F.541 Salt bridges: A:R.509 FBP.4: 16 residues within 4Å: Chain B: 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.452, B:K.453, B:S.454, B:S.457, B:S.457, B:G.534, B:R.536, B:R.536, B:G.538, B:S.539, B:G.540, B:F.541 Salt bridges: B:R.509 FBP.10: 18 residues within 4Å: Chain C: L.451, T.452, K.453, S.454, G.455, S.457, W.502, D.505, R.509, T.533, G.534, R.536, P.537, G.538, S.539, G.540, F.541, T.542 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:G.455, C:S.457, C:R.509, C:R.509, C:G.534, C:G.538, C:S.539, C:G.540, C:F.541, C:T.542 Salt bridges: C:R.509 FBP.12: 19 residues within 4Å: Chain D: L.451, T.452, K.453, S.454, G.455, R.456, S.457, W.502, R.509, T.533, G.534, W.535, R.536, P.537, G.538, S.539, G.540, F.541, T.542 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.452, D:T.452, D:K.453, D:S.454, D:G.455, D:S.457, D:S.457, D:S.457, D:G.534, D:R.536, D:G.538, D:G.540, D:F.541, D:F.541 Salt bridges: D:R.509

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: F.264, K.290, E.292, D.316 Ligands: OXL.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.292, A:D.316 MG.6: 5 residues within 4Å: Chain B: F.264, K.290, E.292, D.316 Ligands: OXL.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.11: 5 residues within 4Å: Chain C: F.264, K.290, E.292, D.316 Ligands: OXL.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.14: 4 residues within 4Å: Chain D: K.290, E.292, D.316 Ligands: OXL.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.292, D:D.316

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

EDO.8: 1 residues within 4Å: Chain C: H.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.226, C:K.226 EDO.9: 3 residues within 4Å: Chain C: H.98, R.140, D.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.140

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