MolNFT v1 · #128344 · protein
Dimer structure of sortilin ectodomain crystal form 3, 4.0 ångström
5NNJ: “Dimer structure of sortilin ectodomain crystal form 3, 4.0 ångström”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.71). MolNFT v1 #128344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NNJ
- Type
- protein
- Length
- 2,590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q6PHU5
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Sortilin | protein | 648 | 5% helix, 41% strand | Q6PHU5 |
| C | Sortilin | protein | 646 | 5% helix, 42% strand | Q6PHU5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, D, C
- BMA · beta-D-mannopyranose · sugar · 8 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.71 | 0.94 | 27 | empty |
| 2 | 109 | 0.70 | 0.92 | 29 | empty |
| 3 | 99 | 0.70 | 0.92 | 28 | empty |
| 4 | 86 | 0.69 | 0.93 | 28 | empty |
| 5 | 597 | 0.68 | 0.77 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2086 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 1927 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 278 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 13 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
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 Q6PHU5
- Elsewhere: RCSB PDB 5NNJ · PDBe 5NNJ · UniProt Q6PHU5
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