MolNFT v1 · #158590 · protein
Crystal structure of glycosylated lysosomal membrane protein (glmp) luminal domain bound to a Fab fragment
6NYQ · 1H3 Fab light chain: “Crystal structure of glycosylated lysosomal membrane protein (glmp) luminal domain bound to a Fab fragment”. X-ray diffraction, 2 ligands (NAG, NA), 4 pockets (best druggability 0.63). MolNFT v1 #158590 on…
- PDB
- 6NYQ
- Type
- protein
- Length
- 746 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1H3 Fab light chain; 1H3 Fab heavy chain; Glycosylated lysosomal membrane protein
- UniProt
- Q9JHJ3
- Ligands
- NAG, NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 1H3 Fab light chain | protein | 212 | 6% helix, 51% strand | — |
| H | 1H3 Fab heavy chain | protein | 215 | 8% helix, 52% strand | — |
| C | Glycosylated lysosomal membrane protein | protein | 319 | 8% helix, 43% strand | Q9JHJ3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C
- NA · Sodium ion · metal · 4 copies · chains H, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.63 | 0.74 | 57 | empty |
| 2 | 53 | 0.55 | 0.90 | 21 | empty |
| 3 | 206 | 0.48 | 0.75 | 42 | empty |
| 4 | 86 | 0.31 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1634 Ų buried · 10 hydrogen bonds · protein-protein
- L–C · 529 Ų buried · 7 hydrogen bonds · protein-protein
- H–C · 440 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6NYQ · Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound… · the same entry in another collection · chain L against L, TM-score 1.00
- Q9JHJ3 · AlphaFold monomer V2.0 prediction for glycosylated lysosomal membrane protein (Q9JHJ3) · a predicted model of the same protein · chain C 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 Q9JHJ3
- Elsewhere: RCSB PDB 6NYQ · PDBe 6NYQ · UniProt Q9JHJ3
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