MolNFT v1 · #84893 · protein
NETRING2 lam and EGF1 domains
3ZYG · Netrin-G2: “NETRING2 lam and EGF1 domains”. X-ray diffraction, 2 ligands (NAG, CA), 7 pockets (best druggability 0.72). MolNFT v1 #84893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZYG
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-G2
- UniProt
- Q96CW9
- Ligands
- NAG, CA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-G2 | protein | 322 | 14% helix, 33% strand | Q96CW9 |
| B | Netrin-G2 | protein | 317 | 13% helix, 31% strand | Q96CW9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.72 | 0.78 | 58 | empty |
| 2 | 108 | 0.53 | 0.82 | 18 | empty |
| 3 | 89 | 0.52 | 0.83 | 17 | empty |
| 4 | 163 | 0.45 | 0.75 | 24 | empty |
| 5 | 98 | 0.38 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 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 Q96CW9
- Elsewhere: RCSB PDB 3ZYG · PDBe 3ZYG · UniProt Q96CW9
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