Research workbench
Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with AF40431
Analyse Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MSL
- Type
- protein
- Length
- 654 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q99523
- Ligands
- 2ET, NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 654 | 7% helix, 39% strand | Q99523 |
Ligands and binding sites
- 2ET · N-[(7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methyl]-L-leucine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.62 | 0.76 | 56 | empty |
| 2 | 127 | 0.42 | 0.76 | 24 | empty |
| 3 | 98 | 0.41 | 0.77 | 17 | 2ET |
| 4 | 51 | 0.27 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4MSL · Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431 · the same entry in another collection · chain A against A, TM-score 1.00
- Q99523 · AlphaFold monomer V2.0 prediction for sortilin (Q99523) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q99523
- Elsewhere: RCSB PDB 4MSL · PDBe 4MSL · UniProt Q99523
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