Research workbench
Crystal structure of the A2B1B2 domains from human neuropilin-1
Analyse Crystal structure of the A2B1B2 domains from human neuropilin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQM
- Type
- protein
- Length
- 436 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-1
- UniProt
- O14786
- Ligands
- NAG, FUC, CA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropilin-1 | protein | 436 | 5% helix, 46% strand | O14786 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.65 | 0.79 | 54 | EDO |
| 2 | 127 | 0.44 | 0.77 | 17 | EDO |
| 3 | 85 | 0.36 | 0.76 | 23 | empty |
| 4 | 55 | 0.28 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
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 2QQM · PDBe 2QQM · UniProt O14786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.