SMTL ID : 4kq2.1

Glucose1,2cyclic phosphate bound activated state of Yeast Glycogen Synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.499 Hydrogen bonds: A:R.339, A:L.500, A:T.533, A:E.536 Salt bridges: A:R.339, A:K.345 pi-Stacking: A:Y.511 U5P.6: 8 residues within 4Å: Chain B: G.338, R.339, K.345, F.499, L.500, Y.511, T.533, E.536 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.499 Hydrogen bonds: B:R.339, B:L.500, B:E.536 Salt bridges: B:R.339, B:K.345 pi-Stacking: B:Y.511 U5P.12: 14 residues within 4Å: Chain C: R.39, G.42, R.339, K.345, V.375, F.499, L.500, Y.511, E.528, G.531, Y.532, T.533, E.536 Ligands: 1S3.11 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.499 Hydrogen bonds: C:R.39, C:R.39, C:L.500, C:E.528, C:E.528, C:Y.532, C:T.533, C:E.536 Salt bridges: C:R.339, C:K.345 pi-Stacking: C:Y.511 U5P.16: 9 residues within 4Å: Chain D: G.338, R.339, K.345, V.375, F.499, L.500, Y.511, T.533, E.536 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.339, D:L.500, D:E.536 Salt bridges: D:R.339, D:K.345 pi-Stacking: D:F.499, 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, R.606 Chain D: H.299, E.300 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.302, A:Q.302, D:E.300 Salt bridges: 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.7: 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 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.302, B:R.599 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.13: 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:N.303, 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.17: 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 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain D Salt bridges: A:H.299, D:H.305, D:H.305, D:K.309, D:H.519, D:R.599, D:R.602, D:R.606, D:R.606 Hydrogen bonds: D:Q.302

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

PEG.3: 3 residues within 4Å: Chain A: K.410, F.413 Chain B: R.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.410 PEG.8: 5 residues within 4Å: Chain A: R.317, E.398 Chain B: G.409, K.410, F.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.317 PEG.14: 4 residues within 4Å: Chain C: K.410, F.413 Chain D: E.310, E.398 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.409, C:K.410, D:E.398 PEG.18: 6 residues within 4Å: Chain C: E.310, R.317, E.398 Chain D: G.409, K.410, F.413 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.317, D:G.409

7 x BA: BARIUM ION(Non-covalent)

BA.4: 1 residues within 4Å: Chain A: Q.57 No protein-ligand interaction detected (PLIP) BA.5: 1 residues within 4Å: Chain A: R.202 No protein-ligand interaction detected (PLIP) BA.9: 2 residues within 4Å: Chain B: Q.57, K.59 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.57 BA.10: 1 residues within 4Å: Chain B: D.558 No protein-ligand interaction detected (PLIP) BA.15: 1 residues within 4Å: Chain C: Q.57 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Q.57 BA.19: 1 residues within 4Å: Chain D: Q.57 No protein-ligand interaction detected (PLIP) BA.20: 1 residues within 4Å: Chain D: D.558 No protein-ligand interaction detected (PLIP)

1 x 1S3: (2R,3aR,5R,6S,7S,7aR)-5-(hydroxymethyl)tetrahydro-3aH-[1,3,2]dioxaphospholo[4,5-b]pyran-2,6,7-triol 2-oxide(Non-covalent)

1S3.11: 11 residues within 4Å: Chain C: G.42, H.212, R.218, N.288, R.339, E.528, P.529, W.530, G.531, Y.532 Ligands: U5P.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.212, C:N.288, C:W.530, C:G.531, C:Y.532 Salt bridges: C:R.218, C:R.339

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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