Research workbench
NETRING1 in complex with NGL1
Analyse NETRING1 in complex with NGL1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYJ
- Type
- protein
- Length
- 1,444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat-containing protein 4C; Netrin-G1
- UniProt
- Q9HCJ2, Q9Y2I2
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Leucine-rich repeat-containing protein 4C | protein | 396 | 4% helix, 24% strand | Q9HCJ2 |
| B, D | Netrin-G1 | protein | 326 | 14% helix, 29% strand | Q9Y2I2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.84 | 0.85 | 93 | empty |
| 2 | 867 | 0.82 | 0.84 | 97 | empty |
| 3 | 164 | 0.63 | 0.85 | 24 | empty |
| 4 | 157 | 0.61 | 0.84 | 27 | empty |
| 5 | 311 | 0.59 | 0.77 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1328 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1308 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 150 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZYJ · NetrinG1 in complex with NGL1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2I2 · AlphaFold monomer V2.0 prediction for netrin-G1 (Q9Y2I2) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9HCJ2 · AlphaFold monomer V2.0 prediction for leucine-rich repeat-containing protein 4C (Q9HCJ2) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q9HCJ2
- Every structure of UniProt Q9Y2I2
- Elsewhere: RCSB PDB 3ZYJ · PDBe 3ZYJ · UniProt Q9HCJ2 · UniProt Q9Y2I2
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