SMTL ID : 6jfb.1

Crystal structure of human pyruvate kinase M2 isoform

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

4 x SER: SERINE(Non-covalent)

SER.1: 8 residues within 4Å: Chain A: R.64, N.65, T.66, N.91, H.485, I.490, F.491, P.492 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.65, A:N.91, A:N.91, A:H.485, A:G.489 Water bridges: A:N.65, A:R.521, A:R.521, S.1 Salt bridges: A:R.64, A:H.485, A:R.521 SER.3: 9 residues within 4Å: Chain B: R.64, N.65, T.66, N.91, H.485, G.489, I.490, F.491, P.492 10 PLIP interactions: 2 Ligand-Ligand interactions, 8 interactions with chain B Hydrogen bonds: S.3, B:N.65, B:N.91, B:H.485, B:G.489, B:I.490 Water bridges: S.3, B:R.521 Salt bridges: B:R.64, B:H.485 SER.5: 9 residues within 4Å: Chain C: R.64, N.65, T.66, N.91, H.485, G.489, I.490, F.491, P.492 15 PLIP interactions: 13 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:R.64, C:N.91, C:H.485, C:G.489, C:I.490, S.5 Water bridges: C:N.65, C:R.521, C:R.521, C:R.521, C:R.521, S.5 Salt bridges: C:R.64, C:H.485, C:R.521 SER.7: 7 residues within 4Å: Chain D: R.64, N.65, N.91, H.485, I.490, F.491, P.492 9 PLIP interactions: 8 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:R.64, D:N.91, D:H.485, D:I.490, S.7 Water bridges: D:N.65, D:R.521 Salt bridges: D:R.64, D:H.485

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

PO4.2: 7 residues within 4Å: Chain A: T.453, K.454, S.455, G.456, R.457, S.458, T.543 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.453, A:K.454, A:S.455, A:G.456, A:R.457, A:S.458, A:T.543 Salt bridges: A:R.457 PO4.4: 6 residues within 4Å: Chain B: T.453, K.454, S.455, G.456, R.457, S.458 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.453, B:K.454, B:S.455, B:G.456, B:R.457, B:S.458, B:S.458, B:S.458 PO4.6: 7 residues within 4Å: Chain C: T.453, K.454, S.455, G.456, R.457, S.458, T.543 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.453, C:T.453, C:K.454, C:S.455, C:G.456, C:S.458, C:S.458

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, T.J. et al., Crystal structure of human pyruvate kinase M2 isoform. To Be Published

Release Date

2020-04-01

Peptides

Pyruvate kinase PKM Isoform M2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate kinase PKM Isoform M2