Research workbench
Crystal structure of chicken netrin-1 (ln-LE3)
Analyse Crystal structure of chicken netrin-1 (ln-LE3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PLM
- Type
- protein
- Length
- 416 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1
- UniProt
- Q90922
- Ligands
- NAG, CA, MG, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 416 | 7% helix, 32% strand | Q90922 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.54 | 0.78 | 30 | CL, MG |
| 2 | 73 | 0.44 | 0.81 | 21 | empty |
Modifications
Observed in the structure: 17 disulfide, 3 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 Q90922
- Elsewhere: RCSB PDB 4PLM · PDBe 4PLM · UniProt Q90922
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