SMTL ID : 4kq1.1

Crystal structure of yeast glycogen synthase in complex with uridine-5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-tetramer

Ligands

4 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 10 residues within 4Å: Chain A: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, Y.532, T.533, E.536 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.499 Hydrogen bonds: A:R.339, A:L.500, A:E.536 Salt bridges: A:R.339, A:K.345 pi-Stacking: A:Y.511 U5P.4: 10 residues within 4Å: Chain B: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, Y.532, T.533, E.536 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.499 Hydrogen bonds: B:R.339, B:L.500, B:T.533, B:E.536 Salt bridges: B:R.339, B:K.345 pi-Stacking: B:Y.511 U5P.7: 12 residues within 4Å: Chain C: R.39, S.45, G.338, R.339, K.345, V.375, F.499, L.500, Y.511, Y.532, T.533, E.536 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:R.39, C:R.39, C:S.45, C:R.339, C:L.500, C:T.533, C:E.536 Salt bridges: C:R.339, C:K.345 pi-Stacking: C:F.499, C:Y.511 U5P.10: 10 residues within 4Å: Chain D: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, Y.532, T.533, E.536 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.499 Hydrogen bonds: D:R.339, D:L.500, D:T.533, D:E.536 Salt bridges: D:R.339, 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 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain A Hydrogen bonds: D:E.300, D:E.300, A:Q.302, A:Q.302 Salt bridges: D:H.299, A:H.305, A:H.305, A:K.309, A:H.519, A:R.599, A:R.602, A:R.606, A:R.606 G6P.5: 10 residues within 4Å: Chain B: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, 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.8: 11 residues within 4Å: Chain B: H.299, E.300 Chain C: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, R.606 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.302, B:E.300 Salt bridges: C:H.305, 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.11: 11 residues within 4Å: Chain A: H.299 Chain D: Q.302, N.303, H.305, A.306, K.309, H.519, R.599, R.602, I.603, R.606 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.302, D:Q.302 Salt bridges: D:H.305, 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: 6 residues within 4Å: Chain A: K.410, F.413 Chain B: E.310, R.317, E.398, V.401 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.310 PEG.6: 3 residues within 4Å: Chain A: 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.9: 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.398, C:K.410 PEG.12: 2 residues within 4Å: Chain C: R.317 Chain D: K.410 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.317

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

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