Research workbench
X-ray structure of neuropilin-1 B1 domain complexed with arg-5 ligand.
Analyse X-ray structure of neuropilin-1 B1 domain complexed with arg-5 ligand. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J1X
- Type
- protein
- Length
- 620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-1
- UniProt
- O14786
- Ligands
- AR5
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Neuropilin-1 | protein | 155 | 6% helix, 49% strand | O14786 |
| B | Neuropilin-1 | protein | 154 | 6% helix, 49% strand | O14786 |
| C | Neuropilin-1 | protein | 156 | 6% helix, 49% strand | O14786 |
Ligands and binding sites
- AR5 · N~2~-(tert-butoxycarbonyl)-L-arginine · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.68 | 0.79 | 55 | empty |
| 2 | 642 | 0.67 | 0.76 | 80 | AR5 |
| 3 | 359 | 0.63 | 0.79 | 33 | empty |
| 4 | 57 | 0.34 | 0.78 | 10 | empty |
| 5 | 58 | 0.26 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 565 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 157 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 O14786
- Elsewhere: RCSB PDB 5J1X · PDBe 5J1X · UniProt O14786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.