Research workbench
Crystal structure of the VPS10P domain of human SORTILIN/NTS3 in complex with neurotensin
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
- 3F6K
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin; Neurotensin
- UniProt
- Q99523, P30990
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 657 | 8% helix, 41% strand | Q99523 |
| N | Neurotensin | protein | 4 | 0% helix, 50% strand | P30990 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- PGE · Triethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.64 | 0.77 | 56 | empty |
| 2 | 119 | 0.41 | 0.76 | 28 | NAG |
| 3 | 57 | 0.26 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–N · 423 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3F6K · Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin · 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
- P30990 · AlphaFold monomer V2.0 prediction for NEUROTENSIN/NEUROMEDIN N (P30990) · a predicted model of the same protein · chain N against A, TM-score 0.72
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
- Every structure of UniProt P30990
- Elsewhere: RCSB PDB 3F6K · PDBe 3F6K · UniProt Q99523 · UniProt P30990
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