Research workbench
The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of dcc
Analyse The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of dcc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4URT
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1; Netrin receptor dcc
- UniProt
- O95631, P43146
- Ligands
- NAG, CA, SO4, CL
- Pockets
- 8 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 420 | 8% helix, 29% strand | O95631 |
| B | Netrin receptor dcc | protein | 206 | 1% helix, 41% strand | P43146 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 17 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.50 | 0.75 | 22 | SO4 |
| 2 | 120 | 0.49 | 0.79 | 22 | empty |
| 3 | 139 | 0.45 | 0.76 | 22 | SO4 |
| 4 | 94 | 0.43 | 0.79 | 23 | empty |
| 5 | 84 | 0.37 | 0.77 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4URT · The crystal structure of a fragment of netrin-1 in complex with FN5- FN6 of DCC · the same entry in another collection · chain A against A, TM-score 1.00
- O95631 · AlphaFold monomer V2.0 prediction for netrin-1 (O95631) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P43146 · AlphaFold monomer V2.0 prediction for netrin receptor dcc (P43146) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 O95631
- Every structure of UniProt P43146
- Elsewhere: RCSB PDB 4URT · PDBe 4URT · UniProt O95631 · UniProt P43146
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