Research workbench
Crystal structure of the human lysosome-associated membrane protein lamp-3 (aka dc-lamp)
Analyse Crystal structure of the human lysosome-associated membrane protein lamp-3 (aka… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AKM
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosome-associated membrane glycoprotein 3
- UniProt
- Q9UQV4
- Ligands
- NAG, IR3
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosome-associated membrane glycoprotein 3 | protein | 155 | 2% helix, 57% strand | Q9UQV4 |
| B | Lysosome-associated membrane glycoprotein 3 | protein | 157 | 2% helix, 62% strand | Q9UQV4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- IR3 · Iridium (III) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.38 | 0.78 | 20 | empty |
| 2 | 73 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4AKM · Crystal structure of the human lysosome-associated membrane protein LAMP-3 (aka DC-LAMP) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UQV4 · AlphaFold monomer V2.0 prediction for lysosome-associated membrane glycoprotein 3 (Q9UQV4) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9UQV4
- Elsewhere: RCSB PDB 4AKM · PDBe 4AKM · UniProt Q9UQV4
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