SMTL ID : 1abb.1

CONTROL OF PHOSPHORYLASE B CONFORMATION BY A MODIFIED COFACTOR: CRYSTALLOGRAPHIC STUDIES ON R-STATE GLYCOGEN PHOSPHORYLASE RECONSTITUTED WITH PYRIDOXAL 5'-DIPHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.2, S.5, R.7, R.60 Chain B: R.34 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.34, A:K.2, A:R.7, A:R.60 Hydrogen bonds: A:S.5 SO4.4: 5 residues within 4Å: Chain A: R.34 Chain B: K.2, S.5, R.7, R.60 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.2, B:S.5 Salt bridges: B:K.2, B:R.7, B:R.60, A:R.34 SO4.7: 6 residues within 4Å: Chain C: K.2, S.5, V.6, R.7, R.60 Chain D: R.34 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Salt bridges: D:R.34, C:K.2, C:R.7, C:R.60 Hydrogen bonds: C:K.2, C:V.6 SO4.10: 5 residues within 4Å: Chain C: R.34 Chain D: K.2, S.5, R.7, R.60 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.5 Salt bridges: D:K.2, D:R.7, D:R.60, C:R.34

4 x PDP: PYRIDOXAL-5'-DIPHOSPHATE(Covalent)

PDP.2: 15 residues within 4Å: Chain A: Y.81, G.126, R.129, W.482, K.559, R.560, K.565, Y.639, R.640, V.641, A.644, G.666, T.667, G.668, K.671 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.129, A:Y.639, A:A.644, A:T.667, A:K.671 Hydrogen bonds: A:R.560, A:T.667, A:G.668 Salt bridges: A:K.559, A:K.559, A:K.565 PDP.5: 14 residues within 4Å: Chain B: Y.81, R.129, W.482, K.559, R.560, K.565, Y.639, R.640, V.641, A.644, G.666, T.667, G.668, K.671 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.644, B:T.667, B:K.671 Hydrogen bonds: B:R.560, B:T.667, B:G.668 Salt bridges: B:K.559, B:K.559, B:R.560, B:K.565 PDP.8: 16 residues within 4Å: Chain C: Y.81, G.126, W.482, V.558, K.559, R.560, K.565, Y.639, R.640, V.641, A.644, E.663, G.666, T.667, G.668, K.671 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.639, C:V.641, C:A.644, C:T.667, C:K.671 Hydrogen bonds: C:R.560, C:Y.639, C:G.668 Salt bridges: C:K.559, C:K.559, C:K.565 PDP.11: 16 residues within 4Å: Chain D: Y.81, G.125, G.126, R.129, W.482, K.559, R.560, K.565, R.640, V.641, A.644, G.666, T.667, G.668, N.669, K.671 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.81, D:R.129, D:V.641, D:T.667, D:K.671 Hydrogen bonds: D:G.126, D:R.560, D:T.667, D:G.668 Salt bridges: D:K.559, D:K.559, D:K.565

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 12 residues within 4Å: Chain A: W.58, Q.62, Q.63, Y.66, E.67, R.233, R.300, R.301, K.306 Chain B: D.33, N.35, V.36 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.35, A:Q.63, A:E.67, A:E.67, A:R.233 Salt bridges: A:R.300, A:R.301 IMP.6: 10 residues within 4Å: Chain A: D.33, N.35, V.36 Chain B: W.58, Y.66, E.67, R.233, R.300, R.301, K.306 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.66, B:R.233, B:K.306 Salt bridges: B:R.300, B:R.301 pi-Stacking: B:Y.66 IMP.9: 11 residues within 4Å: Chain C: Q.62, Y.66, E.67, Y.146, R.233, R.300, R.301, K.306 Chain D: D.33, N.35, V.36 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:N.35, C:R.233, C:K.306 Salt bridges: C:R.300, C:R.301 pi-Stacking: C:Y.66 IMP.12: 12 residues within 4Å: Chain C: D.33, N.35, V.36 Chain D: W.58, I.59, Q.62, Q.63, Y.66, E.67, R.300, R.301, K.306 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.66, D:K.306 Salt bridges: D:R.300, D:R.301 pi-Stacking: D:Y.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leonidas, D.D. et al., Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate. Protein Sci. (1992)

Release Date

1993-10-31

Peptides

GLYCOGEN PHOSPHORYLASE B: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLYCOGEN PHOSPHORYLASE B