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

Structure of the lysosomal domain of limp-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 4 residues within 4Å: Chain A: N.61, V.79, L.125, R.127 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: I.306, P.307, N.318, S.320, I.321, Y.381 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: K.237, C.238, M.240, N.242, Y.260, S.269, D.300, F.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.260 NAG-NAG.5: 5 residues within 4Å: Chain B: N.61, V.79, L.125, R.127, T.163 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain B: V.142, I.306, P.307, L.312, N.318, S.320, I.321, Y.381 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: Y.84, Y.110, V.111, W.171, N.199 No protein-ligand interaction detected (PLIP)

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.2: 8 residues within 4Å: Chain A: Q.56, Y.58, E.78, D.355, R.375, Y.403, N.405, S.407 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain B: K.237, C.238, M.240, N.242, Y.260, S.269, D.300 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(Post Translational Modification)

NAG-NAG-BMA-MAN-NAG.6: 8 residues within 4Å: Chain B: Q.56, Y.58, E.78, D.355, R.375, Y.403, N.405, S.407 No protein-ligand interaction detected (PLIP)

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

NAG.10: 5 residues within 4Å: Chain A: A.109, Y.110, V.111, N.199, G.200 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain A: D.213, S.214, N.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.213 NAG.13: 4 residues within 4Å: Chain B: L.209, D.213, S.214, N.217 No protein-ligand interaction detected (PLIP)

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

PO4.12: 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 PO4.14: 7 residues within 4Å: Chain B: L.194, F.195, K.198, D.265, K.323, M.330, I.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.265 Salt bridges: B:K.323

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Lysosome membrane protein 2

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