SMTL ID : 6pdt.1

cryoEM structure of yeast glucokinase filament

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 17 residues within 4Å: Chain A: S.164, Y.165, P.166, T.181, K.182, N.217, D.218, T.219, I.249, G.253, T.254, N.255, E.289, G.291, H.320, E.323 Ligands: ATP.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.164, A:N.217, A:N.217, A:N.255, A:E.289, A:E.289, A:E.323 Salt bridges: A:K.182, A:H.320 GLC.4: 17 residues within 4Å: Chain B: S.164, Y.165, P.166, T.181, K.182, N.217, D.218, T.219, I.249, G.253, T.254, N.255, E.289, G.291, H.320, E.323 Ligands: ATP.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.164, B:N.217, B:N.217, B:N.255, B:E.289, B:E.289, B:E.323 Salt bridges: B:K.182, B:H.320 GLC.7: 17 residues within 4Å: Chain C: S.164, Y.165, P.166, T.181, K.182, N.217, D.218, T.219, I.249, G.253, T.254, N.255, E.289, G.291, H.320, E.323 Ligands: ATP.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.164, C:N.217, C:N.217, C:N.255, C:E.289, C:E.289, C:E.323 Salt bridges: C:K.182, C:H.320 GLC.10: 17 residues within 4Å: Chain D: S.164, Y.165, P.166, T.181, K.182, N.217, D.218, T.219, I.249, G.253, T.254, N.255, E.289, G.291, H.320, E.323 Ligands: ATP.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.164, D:N.217, D:N.217, D:N.255, D:E.289, D:E.289, D:E.323 Salt bridges: D:K.182, D:H.320

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.92, S.164, D.218, I.249 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218 MG.5: 5 residues within 4Å: Chain B: R.92, S.164, D.218, I.249 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.218 MG.8: 5 residues within 4Å: Chain C: R.92, S.164, D.218, I.249 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.218 MG.11: 5 residues within 4Å: Chain D: R.92, S.164, D.218, I.249 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.218

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 26 residues within 4Å: Chain A: G.87, G.88, T.89, N.90, R.92, S.164, K.182, D.218, I.249, G.251, T.252, G.253, G.328, M.329, S.369, S.370, E.371, S.374, G.450, S.451, V.452, Y.455, Y.456 Chain B: S.394 Ligands: GLC.1, MG.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.164, A:S.164, A:T.252, A:G.253, A:S.370, A:S.370, A:S.370, A:S.374, A:S.451, A:S.451, B:S.394 Salt bridges: A:R.92, A:K.182 ATP.6: 26 residues within 4Å: Chain A: S.394 Chain B: G.87, G.88, T.89, N.90, R.92, S.164, K.182, D.218, I.249, G.251, T.252, G.253, G.328, M.329, S.369, S.370, E.371, S.374, G.450, S.451, V.452, Y.455, Y.456 Ligands: GLC.4, MG.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.164, B:S.164, B:T.252, B:G.253, B:S.370, B:S.370, B:S.370, B:S.374, B:S.451, B:S.451, A:S.394 Salt bridges: B:R.92, B:K.182 ATP.9: 26 residues within 4Å: Chain C: G.87, G.88, T.89, N.90, R.92, S.164, K.182, D.218, I.249, G.251, T.252, G.253, G.328, M.329, S.369, S.370, E.371, S.374, G.450, S.451, V.452, Y.455, Y.456 Chain D: S.394 Ligands: GLC.7, MG.8 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.164, C:S.164, C:T.252, C:G.253, C:S.370, C:S.370, C:S.370, C:S.374, C:S.451, C:S.451, D:S.394 Salt bridges: C:R.92, C:K.182 ATP.12: 26 residues within 4Å: Chain C: S.394 Chain D: G.87, G.88, T.89, N.90, R.92, S.164, K.182, D.218, I.249, G.251, T.252, G.253, G.328, M.329, S.369, S.370, E.371, S.374, G.450, S.451, V.452, Y.455, Y.456 Ligands: GLC.10, MG.11 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.164, D:S.164, D:T.252, D:G.253, D:S.370, D:S.370, D:S.370, D:S.374, D:S.451, D:S.451, C:S.394 Salt bridges: D:R.92, D:K.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stoddard, P.R. et al., Polymerization in the actin ATPase clan regulates hexokinase activity in yeast. Science (2020)

Release Date

2020-03-11

Peptides

Glucokinase-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucokinase-1

Related Entries With Identical Sequence