SMTL ID : 4qgc.1

crystal structure of PKM2-K422R mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: N.79, S.81, D.117, T.118, S.247 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.81, A:D.117, A:T.118, H2O.1, H2O.2 K.6: 5 residues within 4Å: Chain B: N.79, S.81, D.117, T.118, S.247 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.81, B:D.117, B:T.118 K.10: 6 residues within 4Å: Chain C: N.79, S.81, D.117, T.118, S.247, K.274 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.81, C:D.117, C:T.118 K.14: 6 residues within 4Å: Chain D: N.79, S.81, D.117, T.118, S.247, K.274 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.81, D:D.117, D:T.118, H2O.19

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

SO4.2: 5 residues within 4Å: Chain A: K.437, W.486, R.493, P.521, G.522 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.486, A:G.522 Water bridges: A:R.493 Salt bridges: A:K.437, A:R.493 SO4.3: 7 residues within 4Å: Chain A: T.436, K.437, S.438, G.439, R.440, S.441, T.526 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.436, A:T.436, A:K.437, A:S.438, A:G.439, A:R.440, A:S.441, A:S.441, A:T.526 Water bridges: A:S.438 SO4.4: 4 residues within 4Å: Chain A: N.79, S.81, H.82, R.124 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.79 Water bridges: A:R.77, A:R.124, A:R.124, A:G.212 Salt bridges: A:H.82, A:R.124 SO4.7: 7 residues within 4Å: Chain B: T.436, K.437, S.438, G.439, R.440, S.441, T.526 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.436, B:T.436, B:K.437, B:S.438, B:G.439, B:R.440, B:S.441, B:S.441, B:T.526 SO4.8: 3 residues within 4Å: Chain B: K.437, W.486, R.493 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.518 Salt bridges: B:R.493 SO4.11: 7 residues within 4Å: Chain C: T.436, K.437, S.438, G.439, R.440, S.441, T.526 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.437, C:S.438, C:S.438, C:G.439, C:S.441 Salt bridges: C:R.440 SO4.12: 3 residues within 4Å: Chain C: W.486, R.493, G.522 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.522 Salt bridges: C:R.493 SO4.15: 4 residues within 4Å: Chain D: K.437, W.486, R.493, G.522 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.522 Salt bridges: D:K.437, D:R.493 SO4.16: 6 residues within 4Å: Chain D: T.436, K.437, S.438, G.439, R.440, S.441 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.436, D:K.437, D:S.438, D:S.438, D:G.439, D:S.441

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: R.47, N.48, T.49, N.74, R.110, H.468, I.473, F.474, P.475 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.47, A:N.74, A:R.110, A:R.110, A:H.468, A:I.473 Water bridges: A:I.473 GOL.9: 11 residues within 4Å: Chain B: R.47, N.48, T.49, G.50, N.74, R.110, H.468, Y.470, I.473, F.474, P.475 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.74, B:R.110, B:H.468, B:H.468 GOL.13: 6 residues within 4Å: Chain C: R.47, T.49, A.467, H.468, I.473, P.475 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.47, C:A.467 GOL.17: 8 residues within 4Å: Chain D: R.47, N.48, N.74, R.110, H.468, I.473, F.474, P.475 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.47, D:R.110, D:R.110, D:I.473 Water bridges: D:G.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Structural insight into mechanisms for dynamic regulation of PKM2. Protein Cell (2015)

Release Date

2015-02-25

Peptides

Pyruvate kinase PKM: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM