SMTL ID : 4kqm.1

Crystal structure of yeast glycogen synthase E169Q mutant in complex with glucose and UDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-tetramer

Ligands

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 12 residues within 4Å: Chain A: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, E.528, G.531, Y.532, T.533, E.536 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.499 Hydrogen bonds: A:R.339, A:L.500, A:G.531, A:Y.532, A:T.533, A:T.533, A:E.536 Salt bridges: A:R.339, A:K.345, A:K.345 pi-Stacking: A:Y.511 UDP.4: 12 residues within 4Å: Chain B: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, E.528, G.531, Y.532, T.533, E.536 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.499 Hydrogen bonds: B:R.339, B:L.500, B:E.528, B:G.531, B:Y.532, B:T.533, B:T.533, B:E.536 Salt bridges: B:R.339, B:R.339, B:K.345, B:K.345 pi-Stacking: B:Y.511 UDP.9: 18 residues within 4Å: Chain C: R.39, G.41, G.42, S.45, R.218, R.339, K.345, V.375, F.499, L.500, Y.511, E.528, G.531, Y.532, T.533, E.536 Ligands: GLC.7, BGC.8 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.499 Hydrogen bonds: C:G.42, C:S.45, C:R.218, C:L.500, C:G.531, C:Y.532, C:T.533, C:T.533, C:T.533, C:E.536 Salt bridges: C:R.339, C:K.345, C:K.345 pi-Stacking: C:Y.511 UDP.12: 12 residues within 4Å: Chain D: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, E.528, G.531, Y.532, T.533, E.536 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.499 Hydrogen bonds: D:R.339, D:L.500, D:G.531, D:Y.532, D:T.533, D:T.533, D:E.536 Salt bridges: D:R.339, D:K.345, D:K.345 pi-Stacking: D:Y.511

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.2: 11 residues within 4Å: Chain A: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, I.603, R.606 Chain D: H.299 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.302 Salt bridges: A:H.305, A:K.309, A:H.519, A:R.599, A:R.602, A:R.606, A:R.606, D:H.299 G6P.5: 11 residues within 4Å: Chain B: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, I.603, R.606 Chain C: H.299 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.302 Salt bridges: B:H.305, B:K.309, B:H.519, B:R.599, B:R.602, B:R.606, B:R.606, C:H.299 G6P.10: 11 residues within 4Å: Chain B: H.299 Chain C: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, I.603, R.606 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.302 Salt bridges: C:H.305, C:K.309, C:H.519, C:R.599, C:R.602, C:R.606, C:R.606, B:H.299 G6P.13: 10 residues within 4Å: Chain A: H.299 Chain D: Q.302, H.305, A.306, K.309, H.519, R.599, R.602, I.603, R.606 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.302 Salt bridges: D:H.305, D:K.309, D:H.519, D:R.599, D:R.602, D:R.606, D:R.606, A:H.299

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: K.410, F.413 Chain B: E.398 No protein-ligand interaction detected (PLIP) PEG.6: 5 residues within 4Å: Chain A: E.310, R.317, E.398 Chain B: K.410, F.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.310, A:E.398 PEG.11: 5 residues within 4Å: Chain C: K.410, F.413 Chain D: E.310, R.317, E.398 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.310, C:K.410 PEG.14: 5 residues within 4Å: Chain C: E.310, R.317, E.398 Chain D: K.410, F.413 No protein-ligand interaction detected (PLIP)

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

GLC.7: 14 residues within 4Å: Chain C: G.42, I.43, V.46, H.212, R.218, V.266, N.288, E.528, P.529, W.530, G.531, Y.532 Ligands: BGC.8, UDP.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.212, C:R.218, C:R.218, C:N.288, C:N.288, C:E.528, C:W.530, C:G.531, C:Y.532

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.8: 14 residues within 4Å: Chain C: G.42, I.43, V.46, H.212, R.218, V.266, N.288, E.528, P.529, W.530, G.531, Y.532 Ligands: GLC.7, UDP.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.212, C:R.218, C:R.218, C:N.288, C:E.528, C:E.528, C:W.530, C:G.531, C:Y.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chikwana, V.M. et al., Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-12-11

Peptides

Gsy2p: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Gsy2p