MolNFT v1 · #148918 · protein
The crystal structure of a fragment of netrin-1 in complex with a fragment of draxin
6FKQ: “The crystal structure of a fragment of netrin-1 in complex with a fragment of draxin”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 3 pockets (best druggability 0.45). MolNFT v1 #148918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6FKQ
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1; Draxin
- UniProt
- O95631, Q8NBI3
- Ligands
- NAG, CA, SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 415 | 8% helix, 32% strand | O95631 |
| B | Draxin | protein | 19 | 16% helix, 0% strand | Q8NBI3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.45 | 0.81 | 19 | empty |
| 2 | 89 | 0.35 | 0.75 | 15 | empty |
| 3 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 4 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6FKQ · The crystal structure of a fragment of netrin-1 in complex with a fragment of draxin · 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 0.84
- Q8NBI3 · AlphaFold monomer V2.0 prediction for draxin (Q8NBI3) · a predicted model of the same protein · chain B against A, TM-score 0.24
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 Q8NBI3
- Elsewhere: RCSB PDB 6FKQ · PDBe 6FKQ · UniProt O95631 · UniProt Q8NBI3
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