MolNFT v1 · #103692 · protein
Structure of the SORTILIN:NEUROTENSIN complex at excess neurotensin concentration
4PO7: “Structure of the SORTILIN:NEUROTENSIN complex at excess neurotensin concentration”. X-ray diffraction, 2 ligands (NAG, BMA), 4 pockets (best druggability 0.62). MolNFT v1 #103692 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4PO7
- Type
- protein
- Length
- 673 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin; NEUROTENSIN/NEUROMEDIN N
- UniProt
- Q99523, P30990
- Ligands
- NAG, BMA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 658 | 7% helix, 39% strand | Q99523 |
| N | NEUROTENSIN/NEUROMEDIN N | protein | 9 | 0% helix, 56% strand | P30990 |
| P | NEUROTENSIN/NEUROMEDIN N | protein | 6 | 0% helix, 0% strand | P30990 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- 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 | 459 | 0.62 | 0.76 | 62 | empty |
| 2 | 116 | 0.41 | 0.76 | 23 | NAG |
| 3 | 130 | 0.40 | 0.74 | 25 | empty |
| 4 | 103 | 0.37 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–N · 804 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 506 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4PO7 · Structure of the Sortilin:neurotensin complex at excess neurotensin concentration · 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 P against A, TM-score 0.46
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 4PO7 · PDBe 4PO7 · UniProt Q99523 · UniProt P30990
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