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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 2 residues within 4Å: Chain A: Y.15, E.17 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.17, A:E.17, H2O.1 ZN.2: 1 residues within 4Å: Chain A: H.46 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.46, H2O.1, H2O.2, H2O.2, H2O.2 ZN.3: 1 residues within 4Å: Chain A: E.19 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.19, A:E.19 ZN.4: 1 residues within 4Å: Chain A: H.107 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.107, A:H.107, H2O.1, H2O.1, H2O.2 ZN.5: 3 residues within 4Å: Chain A: F.66, D.94, T.96 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.94, A:D.94, A:T.96, H2O.1 ZN.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.7: 1 residues within 4Å: Ligands: ZN.9 No protein-ligand interaction detected (PLIP) ZN.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.9: 1 residues within 4Å: Ligands: ZN.7 No protein-ligand interaction detected (PLIP)

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

NAG.10: 5 residues within 4Å: Chain A: N.5, T.7, T.12, Y.15, V.154 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.154 NAG.11: 5 residues within 4Å: Chain A: N.21, T.37, V.128, K.139, W.141 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.37 Hydrogen bonds: A:N.21 NAG.12: 4 residues within 4Å: Chain A: F.66, 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.13: 3 residues within 4Å: Chain A: N.73, T.75, D.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85 NAG.14: 7 residues within 4Å: Chain A: T.25, Y.26, E.27, Q.31, T.32, N.33, P.135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.25, A:P.135 Hydrogen bonds: A:N.33

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
A

Lysosome-associated membrane glycoprotein 2

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