SMTL ID : 5gv0.1

Crystal structure of the membrane-proximal domain of mouse lysosome-associated membrane protein 1 (LAMP-1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.88 Ligands: NAG.4 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.88, A:R.88, A:R.88, A:R.88, A:R.88 Salt bridges: A:R.88 SO4.2: 4 residues within 4Å: Chain A: G.54, I.55, N.56, L.57 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.55, A:N.56, A:N.56, A:L.57

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

NAG.3: 6 residues within 4Å: Chain A: N.105, S.107, L.108, F.128, V.129, S.130 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.105 NAG.4: 6 residues within 4Å: Chain A: K.61, A.68, E.70, R.88, N.90 Ligands: SO4.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.70, A:R.88 Hydrogen bonds: A:K.61, A:R.88, A:R.88 Water bridges: A:K.61, A:N.90, A:N.90 NAG.5: 4 residues within 4Å: Chain A: N.13, C.53, G.54, I.55 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.13 Water bridges: A:N.12, A:G.54, A:I.55, A:I.55 NAG.6: 4 residues within 4Å: Chain A: N.76, S.78, S.79, K.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.76, A:K.109 Water bridges: A:S.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Terasawa, K. et al., Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes. Biochem.Biophys.Res.Commun. (2016)

Release Date

2016-10-12

Peptides

Lysosome-associated membrane glycoprotein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysosome-associated membrane glycoprotein 1