SMTL ID : 4wj8.1

Human Pyruvate Kinase M2 Mutant C424A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-tetramer

Ligands

4 x OXD: OXALIC ACID(Non-covalent)

OXD.1: 9 residues within 4Å: Chain A: K.290, E.292, M.311, A.313, R.314, G.315, D.316, T.348 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.315, A:D.316 Salt bridges: A:R.93, A:K.290, A:K.290 OXD.8: 8 residues within 4Å: Chain B: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.315, B:D.316, B:T.348, B:T.348, B:T.348 Salt bridges: B:R.93, B:K.290, B:K.290 OXD.14: 8 residues within 4Å: Chain C: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.315, C:D.316 Salt bridges: C:R.93, C:K.290, C:K.290 OXD.18: 8 residues within 4Å: Chain D: K.290, E.292, A.313, R.314, G.315, D.316, T.348 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.315, D:D.316, D:T.348, D:T.348, D:T.348 Water bridges: D:K.290 Salt bridges: D:R.93, D:K.290, D:K.290

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

FBP.2: 18 residues within 4Å: Chain A: L.451, T.452, K.453, S.454, G.455, 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 17 PLIP interactions: 17 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, A:G.534, A:G.538, A:S.539, A:G.540, A:F.541, A:F.541, A:T.542 Salt bridges: A:K.453, A:R.509 FBP.13: 19 residues within 4Å: Chain C: 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 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.452, C:K.453, C:S.454, C:G.455, C:S.457, C:S.457, C:S.457, C:G.534, C:R.536, C:G.538, C:S.539, C:G.540, C:F.541, C:F.541 Water bridges: C:T.542, C:T.542 Salt bridges: C:R.509

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: N.95, S.97, D.133, T.134, E.138, S.263 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.97, A:T.134 K.11: 5 residues within 4Å: Chain B: N.95, S.97, T.134, E.138, S.263 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.97, B:T.134, H2O.2 K.16: 5 residues within 4Å: Chain C: N.95, S.97, D.133, T.134, S.263 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.97, C:T.134 K.22: 6 residues within 4Å: Chain D: N.95, S.97, D.133, T.134, S.263, K.290 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.97, D:T.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.290, E.292, D.316 Ligands: OXD.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.292, A:D.316 MG.10: 4 residues within 4Å: Chain B: K.290, E.292, D.316 Ligands: OXD.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.292, B:D.316 MG.15: 4 residues within 4Å: Chain C: K.290, E.292, D.316 Ligands: OXD.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.292, C:D.316 MG.21: 4 residues within 4Å: Chain D: K.290, E.292, D.316 Ligands: OXD.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.292, D:D.316, H2O.6

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: R.63, N.64, G.66, N.90, H.484, I.489, F.490, P.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.484, A:I.489 GOL.12: 9 residues within 4Å: Chain B: R.63, N.64, G.66, N.90, A.483, H.484, Y.486, I.489, F.490 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.63, B:N.90, B:H.484, B:H.484, B:I.489, B:I.489 GOL.17: 8 residues within 4Å: Chain C: R.63, N.64, T.65, G.66, N.90, H.484, I.489, F.490 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.63, C:N.90, C:H.484, C:H.484 Water bridges: C:G.488 GOL.23: 9 residues within 4Å: Chain D: R.63, N.64, G.66, N.90, A.483, H.484, Y.486, I.489, F.490 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.63, D:R.63, D:H.484, D:Y.486 GOL.24: 8 residues within 4Å: Chain D: P.137, I.139, N.230, L.231, V.236, F.264, R.266, E.320 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:V.229, D:N.230, D:L.231, D:L.231, D:R.266, D:R.266

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

PO4.6: 5 residues within 4Å: Chain A: D.197, L.200, I.201, G.221, S.222 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.197, A:D.197, A:S.222 Salt bridges: C:K.357 PO4.7: 2 residues within 4Å: Chain A: H.98, R.140 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.228 Salt bridges: A:H.98, A:R.140 PO4.19: 5 residues within 4Å: Chain B: K.357 Chain D: L.200, I.201, G.221, S.222 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Salt bridges: B:K.357 Hydrogen bonds: D:S.222, D:S.222

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 8 residues within 4Å: Chain B: T.452, K.453, S.454, G.455, R.456, S.457, S.539, G.540 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.453, B:S.454, B:G.455, B:S.457, B:S.457, B:G.540 Water bridges: B:T.542 SO4.20: 7 residues within 4Å: Chain D: T.452, K.453, S.454, R.456, S.457, S.539, G.540 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.452, D:K.453, D:S.454, D:S.457, D:S.457, D:G.540 Water bridges: D:R.456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, T. et al., Human Pyruvate Kinase M2 Mutant C424A. To Be Published

Release Date

2015-09-30

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM