SMTL ID : 5lrf.1

Crystal structure of Glycogen Phosphorylase b in complex with KS389

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x KS3: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol(Non-covalent)

KS3.1: 20 residues within 4Å: Chain A: E.88, G.135, L.136, L.139, N.282, N.284, F.285, F.286, R.292, H.341, H.377, T.378, A.383, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.284, A:N.484, A:E.672, A:A.673, A:S.674, A:G.675 Water bridges: A:L.136, A:D.283, A:K.574, A:T.676 pi-Cation interactions: A:H.341, A:H.341 KS3.2: 13 residues within 4Å: Chain A: R.60, V.64, W.67, P.188, W.189, E.190, K.191, A.192, P.229 Chain B: F.37, T.38, V.40 Ligands: KS3.7 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.60, A:V.64, A:W.67, A:K.191, A:P.229, B:V.40 Hydrogen bonds: A:R.60, A:E.190, A:K.191, A:A.192, A:A.192 pi-Cation interactions: A:R.60, A:K.191 KS3.6: 20 residues within 4Å: Chain B: E.88, G.135, L.136, L.139, N.282, N.284, F.285, F.286, R.292, H.341, H.377, T.378, A.383, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.284, B:H.377, B:N.484, B:A.673, B:S.674, B:G.675 Water bridges: B:L.136, B:D.283, B:K.574, B:T.676 pi-Cation interactions: B:H.341, B:H.341 KS3.7: 13 residues within 4Å: Chain A: F.37, T.38, V.40 Chain B: R.60, V.64, W.67, P.188, W.189, E.190, K.191, A.192, P.229 Ligands: KS3.2 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:V.40, B:R.60, B:V.64, B:W.67, B:K.191, B:P.229 Hydrogen bonds: B:R.60, B:E.190, B:K.191, B:A.192, B:A.192 pi-Cation interactions: B:R.60, B:K.191

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 3 residues within 4Å: Chain A: R.309, R.310 Ligands: DMS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.309, A:R.309 DMS.4: 3 residues within 4Å: Chain A: Y.75 Chain B: V.45 Ligands: DMS.3 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.75 DMS.8: 3 residues within 4Å: Chain B: R.309, R.310 Ligands: DMS.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.309, B:R.309 DMS.9: 3 residues within 4Å: Chain A: V.45 Chain B: Y.75 Ligands: DMS.8 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.75

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

PLP.5: 15 residues within 4Å: Chain A: Y.90, G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.648, A:V.650, A:K.680 Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.568, A:K.574, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.10: 15 residues within 4Å: Chain B: Y.90, G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.90, B:Y.648, B:V.650, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.568, B:K.574, B:N.678 Salt bridges: B:K.568, B:K.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kantsadi, A.L. et al., van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. J. Struct. Biol. (2017)

Release Date

2017-06-14

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogen phosphorylase, muscle form

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