SMTL ID : 3e3n.6 (5 other biounits)

The Glycogen phosphorylase b R state- AMP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 9 residues within 4Å: Chain A: W.67, Q.71, Q.72, Y.75, R.309, R.310 Chain B: D.42, N.44, V.45 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.309, A:R.310 pi-Stacking: A:Y.75, A:Y.75 Hydrogen bonds: B:D.42 AMP.4: 12 residues within 4Å: Chain A: D.42, N.44, V.45 Chain B: W.67, Q.71, Y.75, R.309, R.310, K.315, F.316, G.317, C.318 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.75, B:K.315, B:G.317, B:C.318, A:D.42 Water bridges: B:R.242 Salt bridges: B:R.309, B:R.310 pi-Stacking: B:Y.75, B:Y.75, B:F.316 AMP.7: 13 residues within 4Å: Chain C: W.67, Q.71, Y.75, R.242, R.309, R.310, K.315, F.316, G.317, C.318 Chain D: D.42, N.44, V.45 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.315, C:G.317, D:D.42 Water bridges: C:R.242 Salt bridges: C:R.309, C:R.310 pi-Stacking: C:Y.75, C:Y.75 AMP.10: 12 residues within 4Å: Chain C: D.42, N.44, V.45 Chain D: W.67, Q.71, Y.75, R.309, R.310, K.315, F.316, G.317, C.318 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.75, D:K.315, D:G.317, D:C.318, C:D.42 Salt bridges: D:R.309, D:R.310 pi-Stacking: D:Y.75, D:Y.75

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: K.11, S.14, R.16, R.69 Chain B: R.43 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.14, A:S.14 Water bridges: A:V.15 Salt bridges: A:R.16, A:R.69, B:R.43 SO4.3: 3 residues within 4Å: Chain A: G.135, R.569, K.680 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.135 Salt bridges: A:R.569, A:K.574 SO4.5: 5 residues within 4Å: Chain A: R.43 Chain B: K.11, S.14, R.16, R.69 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.11, B:S.14 Salt bridges: B:R.16, B:R.69, A:R.43 SO4.6: 5 residues within 4Å: Chain B: G.134, G.135, R.569, K.574, K.680 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.135 Water bridges: B:R.569, B:R.569 Salt bridges: B:R.569, B:K.574 SO4.8: 4 residues within 4Å: Chain C: S.14, R.16, R.69 Chain D: R.43 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.13 Water bridges: C:Q.72, C:Q.72 Salt bridges: C:R.16, C:R.69, D:R.43 SO4.9: 5 residues within 4Å: Chain C: G.134, G.135, R.569, K.574, K.680 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.135 Salt bridges: C:R.569, C:K.574 SO4.11: 5 residues within 4Å: Chain C: R.43 Chain D: K.11, S.14, R.16, R.69 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.11, D:S.14, D:V.15 Salt bridges: D:R.16, D:R.69, C:R.43 SO4.12: 6 residues within 4Å: Chain D: N.133, G.135, L.136, R.569, Y.573, K.574 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.133, D:G.135, D:L.136, D:Y.573 Salt bridges: D:R.569, D:K.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leonidas, D.D. et al., Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators. Acta Crystallogr.,Sect.F (2021)

Release Date

2009-08-18

Peptides

Glycogen phosphorylase, muscle form: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Glycogen phosphorylase, muscle form

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