SMTL ID : 3fro.1

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 4 residues within 4Å: Chain A: P.14, V.15, K.16, R.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.16 TRS.2: 6 residues within 4Å: Chain A: Y.91, L.98, W.131, H.132, R.154, N.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.91, A:W.131, A:R.154 TRS.5: 5 residues within 4Å: Chain B: R.57, G.60, R.107, H.166, E.167 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.60, B:R.107, B:E.167 Water bridges: B:F.59

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: I.201, W.204, F.435, I.438 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.204 PO4.6: 4 residues within 4Å: Chain B: I.201, W.204, A.434, I.438 No protein-ligand interaction detected (PLIP) PO4.7: 3 residues within 4Å: Chain C: I.201, W.204, D.436 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.436

1 x NHF: 1,5-anhydro-D-fructose(Non-covalent)

NHF.4: 11 residues within 4Å: Chain B: G.19, L.20, A.23, H.153, N.219, K.265, E.341, P.342, F.343, G.344, L.345 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.19, B:H.153, B:K.265, B:F.343, B:G.344, B:L.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz, A. et al., Lyase activity of glycogen synthase: Is an elimination/addition mechanism a possible reaction pathway for retaining glycosyltransferases?. IUBMB Life (2012)

Release Date

2010-01-12

Peptides

GlgA glycogen synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GlgA glycogen synthase