Research workbench
Structure of the dcc-draxin complex
Analyse Structure of the dcc-draxin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z5K
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin receptor dcc; Draxin
- UniProt
- Q63155, D3ZDG4
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin receptor dcc | protein | 380 | 3% helix, 52% strand | Q63155 |
| B | Draxin | protein | 66 | 9% helix, 32% strand | D3ZDG4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.69 | 0.78 | 59 | empty |
| 2 | 58 | 0.50 | 0.86 | 15 | empty |
| 3 | 67 | 0.40 | 0.80 | 16 | empty |
| 4 | 82 | 0.38 | 0.78 | 21 | empty |
| 5 | 70 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1087 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 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 Q63155
- Every structure of UniProt D3ZDG4
- Elsewhere: RCSB PDB 5Z5K · PDBe 5Z5K · UniProt Q63155 · UniProt D3ZDG4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.