SMTL ID : 4q4b.1

Crystal structure of LIMP-2 (space group C2221)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: N.44, V.62, L.108, R.110, T.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.146

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: L.70, Y.93, V.94, W.154, N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.280, C.294, L.295, R.324 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: K.220, C.221, M.223, N.225, Y.243, S.252, D.283, F.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.220

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5: 8 residues within 4Å: Chain A: V.125, H.126, I.289, N.301, S.303, I.304, Y.364 Ligands: NA.10 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain A: Q.39, Y.41, E.61, D.338, R.358, Y.386, N.388, S.390 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.41 Hydrogen bonds: A:Y.41

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 2 residues within 4Å: Chain A: N.21, F.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.21 NAG.8: 5 residues within 4Å: Chain A: L.192, D.196, S.197, N.200, K.203 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.192

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: L.368, F.371, T.374, G.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.368, A:T.374, A:G.375 NA.10: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Lysosome sorting of beta-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor. Nat Commun (2014)

Release Date

2014-07-30

Peptides

Lysosome membrane protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosome membrane protein 2