SMTL ID : 4f7b.1 (3 other biounits)

Structure of the lysosomal domain of limp-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 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

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: N.61, V.79, L.125, R.127, T.163 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG.2: 8 residues within 4Å: Chain A: Q.56, Y.58, E.78, D.355, R.375, Y.403, N.405, S.407 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354

2 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: 6 residues within 4Å: Chain A: K.237, C.238, M.240, N.242, Y.260, S.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 8 residues within 4Å: Chain A: E.138, I.306, P.307, L.312, N.318, S.320, I.321, Y.381 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: 6 residues within 4Å: Chain A: Y.84, L.87, Y.110, V.111, W.171, N.199 No protein-ligand interaction detected (PLIP)

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

NAG.6: 2 residues within 4Å: Chain A: N.38, E.47 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain A: N.297, C.311, L.312 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: L.209, D.213, S.214, N.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.213, A:S.214, A:N.217

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

PO4.9: 6 residues within 4Å: Chain A: L.194, K.198, D.265, K.323, M.330, I.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.265 Salt bridges: A:K.323

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: G.246, V.261, T.358, K.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.246, A:K.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neculai, D. et al., Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36. Nature (2013)

Release Date

2013-10-09

Peptides

Lysosome membrane protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosome membrane protein 2

Related Entries With Identical Sequence