SMTL ID : 6gpb.1

REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC-GLC.1: 13 residues within 4Å: Chain A: Y.404, E.405, N.407, Q.408, L.411, V.422, D.423, L.425, R.426, S.429, V.431, E.433, K.437 No protein-ligand interaction detected (PLIP) GLC-GLC-GLC-GLC-GLC.6: 13 residues within 4Å: Chain B: Y.404, E.405, N.407, Q.408, L.411, V.422, D.423, L.425, R.426, S.429, V.431, E.433, K.437 No protein-ligand interaction detected (PLIP)

2 x H2P: 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose(Non-covalent)

H2P.2: 16 residues within 4Å: Chain A: G.135, L.136, L.139, H.377, T.378, V.455, N.484, R.569, Y.573, K.574, E.672, A.673, S.674, G.675, T.676 Ligands: PLP.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.377 Hydrogen bonds: A:G.135, A:L.136, A:N.484, A:R.569, A:Y.573, A:E.672, A:E.672, A:E.672, A:A.673, A:S.674, A:G.675, A:G.675 Water bridges: A:T.676 Salt bridges: A:R.569, A:K.574 H2P.7: 16 residues within 4Å: Chain B: G.135, L.136, L.139, H.377, T.378, V.455, N.484, R.569, Y.573, K.574, E.672, A.673, S.674, G.675, T.676 Ligands: PLP.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.377 Hydrogen bonds: B:G.135, B:L.136, B:H.377, B:N.484, B:R.569, B:Y.573, B:E.672, B:E.672, B:A.673, B:S.674, B:G.675, B:G.675 Water bridges: B:T.676 Salt bridges: B:R.569, B:K.574

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.3: 16 residues within 4Å: Chain A: Y.90, G.134, G.135, R.138, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 Ligands: H2P.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.648, A:V.650, A:T.676, A:K.680 Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:Y.90, A:K.568, A:K.568 Salt bridges: A:K.568, A:K.574 PLP.8: 16 residues within 4Å: Chain B: Y.90, G.134, G.135, R.138, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 Ligands: H2P.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.648, B:V.650, B:T.676, B:K.680 Hydrogen bonds: B:T.676, B:G.677, B:K.680 Water bridges: B:K.568, B:K.568 Salt bridges: B:K.568, B:K.574

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 5 residues within 4Å: Chain A: F.285, E.572, G.612, Y.613, M.615 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.571, A:E.572, A:M.615 AMP.5: 5 residues within 4Å: Chain A: Y.75, R.309, R.310 Chain B: N.44, V.45 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.309, A:R.310 pi-Stacking: A:Y.75 AMP.9: 5 residues within 4Å: Chain B: F.285, E.572, G.612, Y.613, M.615 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.571, B:M.615 AMP.10: 5 residues within 4Å: Chain A: N.44, V.45 Chain B: Y.75, R.309, R.310 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.309, B:R.310 pi-Stacking: B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, L.N. et al., Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex. J.Mol.Biol. (1990)

Release Date

1992-10-15

Peptides

GLYCOGEN PHOSPHORYLASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE B

Related Entries With Identical Sequence