SMTL ID : 4q4f.1

Crystal structure of LIMP-2 (space group C2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

2 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.1: 5 residues within 4Å: Chain A: N.44, V.62, L.108, R.110, T.146 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain A: Q.39, Y.41, E.61, P.64, E.337, D.338, R.358, Y.386, N.388, S.390 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.41

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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

NAG-NAG-BMA-MAN-MAN-MAN.2: 5 residues within 4Å: Chain A: L.70, Y.93, V.94, W.154, N.182 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.70

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

NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: K.220, C.221, M.223, N.225, Y.243, S.252 No protein-ligand interaction detected (PLIP)

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

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- MAN- MAN- M6D- MAN: 6-O-phosphono-beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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

NAG-NAG-BMA-MAN-MAN-M6D-MAN.5: 12 residues within 4Å: Chain A: V.125, H.126, L.128, R.129, E.130, I.131, I.289, P.290, N.301, S.303, I.304, Y.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.126, A:E.130, A:E.130, A:I.131

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 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: L.192, D.196, S.197, N.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.196, A:N.200

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 2 residues within 4Å: Chain A: Q.264, H.392 Ligand excluded by 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

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