Research workbench
Crystal structure of the A2B1B2 domains from human neuropilin-2
Analyse Crystal structure of the A2B1B2 domains from human neuropilin-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQO
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-2
- UniProt
- O60462
- Ligands
- CA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropilin-2 | protein | 431 | 4% helix, 46% strand | O60462 |
| B | Neuropilin-2 | protein | 426 | 4% helix, 47% strand | O60462 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.74 | 0.90 | 31 | EDO |
| 2 | 431 | 0.72 | 0.83 | 53 | empty |
| 3 | 128 | 0.47 | 0.78 | 20 | empty |
| 4 | 159 | 0.47 | 0.77 | 24 | empty |
| 5 | 115 | 0.44 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 203 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 O60462
- Elsewhere: RCSB PDB 2QQO · PDBe 2QQO · UniProt O60462
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