Research workbench
Crystal structure of the N-terminal leucine rich repeats of netrin-G ligand-3
Analyse Crystal structure of the N-terminal leucine rich repeats of netrin-G ligand-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYN
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat-containing protein 4B
- UniProt
- P0C192
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing protein 4B | protein | 310 | 7% helix, 18% strand | P0C192 |
| B | Leucine-rich repeat-containing protein 4B | protein | 312 | 10% helix, 18% strand | P0C192 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.61 | 0.77 | 30 | empty |
| 2 | 269 | 0.51 | 0.75 | 22 | empty |
| 3 | 52 | 0.41 | 0.82 | 14 | NAG |
| 4 | 64 | 0.38 | 0.79 | 14 | NAG |
Interfaces
1 interface between chains.
- A–B · 353 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZYN · Crystal structure of the N-terminal leucine rich repeats of Netrin-G Ligand-3 · the same entry in another collection · chain B against B, TM-score 1.00
- P0C192 · AlphaFold monomer V2.0 prediction for leucine-rich repeat-containing protein 4B (P0C192) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0C192
- Elsewhere: RCSB PDB 3ZYN · PDBe 3ZYN · UniProt P0C192
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