SMTL ID : 4rkk.1

Structure of a product bound phosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

3 x GLC- 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-(1-4)-alpha-D-glucopyranose(Non-functional Binders)

GLC-GLC-GLC-GLC-GLC-GLC.1: 20 residues within 4Å: Chain A: M.142, T.145, T.146, Y.149, D.200, P.237, D.238, M.239, S.240, R.244, N.270, A.271, V.273, G.274, R.275, Y.307 Ligands: GLC-GLC-GLC.2, GLC-GLC-GLC.2, GLC-GLC-GLC.2, PO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.239, A:Y.307 Water bridges: A:T.241 GLC-GLC-GLC-GLC-GLC-GLC.3: 8 residues within 4Å: Chain A: W.35, K.90, W.102, N.105, G.106, P.107, D.110 Ligands: GLC.8 No protein-ligand interaction detected (PLIP) GLC-GLC-GLC-GLC-GLC-GLC.4: 19 residues within 4Å: Chain B: M.142, T.145, T.146, D.200, P.237, D.238, M.239, S.240, R.244, N.270, A.271, V.273, G.274, R.275, Y.307 Ligands: GLC-GLC-GLC.5, GLC-GLC-GLC.5, GLC-GLC-GLC.5, PO4.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.239 Water bridges: B:T.241

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

GLC-GLC-GLC.2: 3 residues within 4Å: Chain A: W.199 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC.1 No protein-ligand interaction detected (PLIP) GLC-GLC-GLC.5: 3 residues within 4Å: Chain B: W.199 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4 No protein-ligand interaction detected (PLIP)

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-functional Binders)

GLC-GLC-GLC-GLC.6: 7 residues within 4Å: Chain B: W.35, K.90, W.102, N.105, G.106, P.107, D.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.110

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

PO4.7: 11 residues within 4Å: Chain A: D.238, S.269, N.270, A.271, G.272, V.273, G.274, R.275 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.238, A:D.238, A:S.269, A:N.270, A:A.271, A:G.272, A:V.273, A:G.274, A:R.275 Salt bridges: A:R.275 PO4.9: 11 residues within 4Å: Chain B: D.238, S.269, N.270, A.271, G.272, V.273, G.274, R.275 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.238, B:S.269, B:N.270, B:A.271, B:G.272, B:V.273, B:G.274, B:R.275 Salt bridges: B:R.275

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.8: 5 residues within 4Å: Chain A: S.28, W.35, W.88 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC-GLC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.35 GLC.10: 3 residues within 4Å: Chain B: S.28, W.35, W.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raththagala, M. et al., Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease. Mol.Cell (2015)

Release Date

2015-01-07

Peptides

Laforin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Laforin