SMTL ID : 5gv3.2 (1 other biounit)

Crystal structure of the membrane-distal domain of mouse lysosome-associated membrane protein 2 (LAMP-2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.84, D.85 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.84, A:H.84, A:D.85, A:D.85, H2O.1 ZN.2: 3 residues within 4Å: Chain A: K.124, H.144, E.158 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.144, A:E.158 ZN.3: 2 residues within 4Å: Chain A: D.1, E.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.1, A:E.17 ZN.4: 2 residues within 4Å: Chain A: H.46 Ligands: ZN.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.46, H2O.1, H2O.2, H2O.2 ZN.5: 2 residues within 4Å: Chain A: H.46 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.46, H2O.1, H2O.1, H2O.2, H2O.2 ZN.6: 1 residues within 4Å: Chain A: E.19 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.19, A:E.19, H2O.1

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

NAG.7: 3 residues within 4Å: Chain A: N.5, T.12, Y.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.15 NAG.8: 3 residues within 4Å: Chain A: N.91, S.93, V.106 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.106 Hydrogen bonds: A:N.91 NAG.9: 2 residues within 4Å: Chain A: S.57, N.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.57 NAG.10: 6 residues within 4Å: Chain A: T.25, Y.26, E.27, Q.31, N.33, P.135 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.25, A:P.135 Hydrogen bonds: A:Q.31, A:N.33 NAG.11: 5 residues within 4Å: Chain A: N.21, T.37, V.128, K.139, W.141 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.128, A:W.141 Hydrogen bonds: A:N.21

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

2017-09-06

Peptides

Lysosome-associated membrane glycoprotein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Lysosome-associated membrane glycoprotein 2

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