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Crystal structure of the membrane-distal domain of mouse lysosome-associated membrane protein 2 (LAMP-2)
Analyse Crystal structure of the membrane-distal domain of mouse lysosome-associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GV3
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.096
- Source
- Mus musculus
- Molecule
- Lysosome-associated membrane glycoprotein 2
- UniProt
- P17047
- Ligands
- NAG, ZN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.096 · 2 distinct chains · 1% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosome-associated membrane glycoprotein 2 | protein | 161 | 2% helix, 58% strand | P17047 |
| B | Lysosome-associated membrane glycoprotein 2 | protein | 163 | 0% helix, 58% strand | P17047 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- ZN · Zinc ion · metal · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.77 | 0.94 | 25 | empty |
| 2 | 168 | 0.77 | 0.92 | 24 | empty |
| 3 | 290 | 0.49 | 0.73 | 36 | NAG |
Interfaces
1 interface between chains.
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5GV3 · Crystal structure of the membrane-distal domain of mouse lysosome- associated membrane… · the same entry in another collection · chain A against A, TM-score 1.00
- P17047 · AlphaFold monomer V2.0 prediction for lysosome-associated membrane glycoprotein 2 (P17047) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P17047
- Elsewhere: RCSB PDB 5GV3 · PDBe 5GV3 · UniProt P17047
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