Research workbench
NETRING2 in complex with NGL2
Analyse NETRING2 in complex with NGL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYI
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat-containing protein 4; Netrin-G2
- UniProt
- Q9HBW1, Q96CW9
- Ligands
- NAG, CA, PO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing protein 4 | protein | 395 | 4% helix, 23% strand | Q9HBW1 |
| B | Netrin-G2 | protein | 303 | 9% helix, 31% strand | Q96CW9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.71 | 0.79 | 67 | empty |
| 2 | 286 | 0.63 | 0.81 | 43 | PO4 |
| 3 | 251 | 0.54 | 0.76 | 31 | empty |
| 4 | 75 | 0.50 | 0.84 | 15 | empty |
| 5 | 110 | 0.50 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZYI · NetrinG2 in complex with NGL2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HBW1 · AlphaFold monomer V2.0 prediction for leucine-rich repeat-containing protein 4 (Q9HBW1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q96CW9 · AlphaFold monomer V2.0 prediction for netrin-G2 (Q96CW9) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9HBW1
- Every structure of UniProt Q96CW9
- Elsewhere: RCSB PDB 3ZYI · PDBe 3ZYI · UniProt Q9HBW1 · UniProt Q96CW9
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