MolNFT v1 · #79714 · protein
Crystal structure of domain VI and LE1 of human netrin-G2
3TBD: “Crystal structure of domain VI and LE1 of human netrin-G2”. X-ray diffraction, 4 ligands (NAG, CA, PO4), 4 pockets (best druggability 0.57). MolNFT v1 #79714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TBD
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-G2
- UniProt
- Q96CW9
- Ligands
- NAG, CA, PO4, CL
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-G2 | protein | 331 | 13% helix, 32% strand | Q96CW9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.57 | 0.84 | 19 | empty |
| 2 | 102 | 0.47 | 0.80 | 19 | empty |
| 3 | 79 | 0.38 | 0.77 | 16 | empty |
| 4 | 50 | 0.38 | 0.81 | 16 | PO4 |
Modifications
Observed in the structure: 8 disulfide, 2 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 3TBD · PDBe 3TBD · UniProt Q96CW9
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