MolNFT v1 · #103605 · protein
Crystal structure of chicken netrin-1 (ln-LE3) in complex with mouse dcc (FN4-5)
4PLO · Netrin receptor dcc: “Crystal structure of chicken netrin-1 (ln-LE3) in complex with mouse dcc (FN4-5)”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 6 pockets (best druggability 0.61). MolNFT v1 #103605 on GenesisL1: 3D structure…
- PDB
- 4PLO
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin receptor dcc; Netrin-1
- UniProt
- P70211, Q90922
- Ligands
- NAG, CA, SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Netrin receptor dcc | protein | 192 | 2% helix, 48% strand | P70211 |
| A | Netrin-1 | protein | 412 | 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
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.61 | 0.77 | 43 | empty |
| 2 | 163 | 0.61 | 0.83 | 30 | empty |
| 3 | 262 | 0.60 | 0.79 | 45 | empty |
| 4 | 75 | 0.36 | 0.76 | 14 | empty |
| 5 | 58 | 0.35 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 723 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4PLO · Crystal Structure of chicken Netrin-1 (LN-LE3) in complex with mouse DCC (FN4-5) · the same entry in another collection · chain B against B, TM-score 1.00
- Q90922 · AlphaFold monomer V2.0 prediction for netrin-1 (Q90922) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P70211 · AlphaFold monomer V2.0 prediction for netrin receptor dcc (P70211) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 P70211
- Every structure of UniProt Q90922
- Elsewhere: RCSB PDB 4PLO · PDBe 4PLO · UniProt P70211 · UniProt Q90922
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