Research workbench
X-ray structure of neuropilin-1 B1 domain complexed with arg-6 ligand.
Analyse X-ray structure of neuropilin-1 B1 domain complexed with arg-6 ligand. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JHK
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-1
- UniProt
- O14786
- Ligands
- 6K8
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropilin-1 | protein | 154 | 6% helix, 48% strand | O14786 |
| B | Neuropilin-1 | protein | 158 | 6% helix, 48% strand | O14786 |
Ligands and binding sites
- 6K8 · N-(benzenecarbonyl)glycyl-L-arginine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.51 | 0.77 | 32 | empty |
| 2 | 90 | 0.38 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 395 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 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 5JHK · PDBe 5JHK · UniProt O14786
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