MolNFT v1 · #100764 · protein
Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with AF38469
4N7E: “Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with AF38469”. X-ray diffraction, 3 ligands (2JQ, NAG, BMA), 6 pockets (best druggability 0.64). MolNFT v1 #100764 on GenesisL1: 3D structure, binding sites…
- PDB
- 4N7E
- Type
- protein
- Length
- 653 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q99523
- Ligands
- 2JQ, NAG, BMA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 653 | 7% helix, 40% strand | Q99523 |
Ligands and binding sites
- 2JQ · 2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.64 | 0.77 | 69 | empty |
| 2 | 139 | 0.41 | 0.75 | 24 | NAG |
| 3 | 84 | 0.41 | 0.78 | 15 | 2JQ |
| 4 | 53 | 0.35 | 0.79 | 21 | PGE |
| 5 | 80 | 0.30 | 0.73 | 19 | empty |
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4N7E · Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469 · 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 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 Q99523
- Elsewhere: RCSB PDB 4N7E · PDBe 4N7E · UniProt Q99523
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