Research workbench
Dimer structure of sortilin ectodomain crystal form 1, 2.3A
Analyse Dimer structure of sortilin ectodomain crystal form 1, 2.3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NMT
- Type
- protein
- Length
- 1,311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortilin
- UniProt
- Q6PHU5
- Ligands
- NAG, BMA, CL
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortilin | protein | 654 | 6% helix, 42% strand | Q6PHU5 |
| B | Sortilin | protein | 657 | 6% helix, 42% strand | Q6PHU5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.71 | 0.96 | 25 | empty |
| 2 | 74 | 0.68 | 0.94 | 26 | empty |
| 3 | 611 | 0.68 | 0.77 | 74 | empty |
| 4 | 666 | 0.66 | 0.75 | 71 | empty |
| 5 | 469 | 0.63 | 0.76 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 2324 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-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 5NMT · PDBe 5NMT · UniProt Q6PHU5
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