SMTL ID : 5vnc.1

Glycogen synthase in complex with UDP and glucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 Å

Oligo State

homo-tetramer

Ligands

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

UDP.1: 12 residues within 4Å: Chain A: G.339, R.340, K.346, V.376, F.500, L.501, Y.512, E.529, G.532, Y.533, T.534, E.537 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.340, A:L.501, A:G.532, A:Y.533, A:T.534, A:E.537 Salt bridges: A:K.346, A:K.346 pi-Stacking: A:F.500, A:Y.512 UDP.3: 13 residues within 4Å: Chain B: A.338, G.339, R.340, K.346, V.376, F.500, L.501, Y.512, E.529, G.532, Y.533, T.534, E.537 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.500 Hydrogen bonds: B:R.340, B:L.501, B:E.529, B:Y.533, B:T.534, B:T.534, B:E.537 Salt bridges: B:K.346, B:K.346 pi-Stacking: B:Y.512 UDP.6: 17 residues within 4Å: Chain C: R.40, G.42, G.43, S.46, R.219, R.340, K.346, V.376, F.500, L.501, Y.512, E.529, G.532, Y.533, T.534, E.537 Ligands: GCS.5 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.500 Hydrogen bonds: C:G.43, C:S.46, C:R.219, C:L.501, C:Y.533, C:T.534, C:T.534, C:E.537 Salt bridges: C:R.340, C:K.346, C:K.346 pi-Stacking: C:Y.512 UDP.8: 12 residues within 4Å: Chain D: G.339, R.340, K.346, V.376, F.500, L.501, Y.512, E.529, G.532, Y.533, T.534, E.537 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.500 Hydrogen bonds: D:R.340, D:L.501, D:G.532, D:Y.533, D:T.534, D:T.534, D:E.537 Salt bridges: D:K.346, D:K.346 pi-Stacking: D:Y.512

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

G6P.2: 11 residues within 4Å: Chain A: Q.303, N.304, H.306, A.307, K.310, H.520, R.600, R.603, I.604, R.607 Chain D: H.300 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.303, A:Q.303 Salt bridges: A:H.306, A:H.306, A:K.310, A:H.520, A:R.600, A:R.603, A:R.607, A:R.607, D:H.300 G6P.4: 10 residues within 4Å: Chain B: Q.303, N.304, H.306, A.307, K.310, H.520, R.600, R.603, R.607 Chain C: H.300 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.303, B:Q.303 Salt bridges: B:H.306, B:K.310, B:H.520, B:R.600, B:R.603, B:R.607, B:R.607, C:H.300 G6P.7: 11 residues within 4Å: Chain B: H.300 Chain C: Q.303, N.304, H.306, A.307, K.310, H.520, R.600, R.603, I.604, R.607 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.303 Salt bridges: C:H.306, C:H.306, C:K.310, C:H.520, C:R.600, C:R.603, C:R.607, C:R.607, B:H.300 G6P.9: 12 residues within 4Å: Chain A: Q.297, H.300 Chain D: Q.303, N.304, H.306, A.307, K.310, H.520, R.600, R.603, I.604, R.607 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:Q.303, D:Q.303, A:Q.297 Salt bridges: D:H.306, D:K.310, D:H.520, D:R.600, D:R.603, D:R.607, D:R.607, A:H.300

1 x GCS: 2-amino-2-deoxy-beta-D-glucopyranose(Non-covalent)

GCS.5: 13 residues within 4Å: Chain C: G.43, I.44, H.213, R.219, V.267, N.289, K.346, E.529, P.530, W.531, G.532, Y.533 Ligands: UDP.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.213, C:R.219, C:R.219, C:N.289, C:K.346, C:K.346, C:E.529, C:W.531, C:G.532, C:Y.533 Salt bridges: C:R.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahalingan, K.K. et al., Glycogen synthase in complex with UDP and glucosamine. To Be Published

Release Date

2018-05-02

Peptides

Glycogen [starch] synthase isoform 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycogen [starch] synthase isoform 2

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