Research workbench
Neuropilin-2 A1A2B1B2 domains in complex with a semaphorin-blocking Fab
Analyse Neuropilin-2 A1A2B1B2 domains in complex with a semaphorin-blocking Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQL
- Type
- protein
- Length
- 990 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-2; Antibody heavy chain; Antibody light chain
- UniProt
- O60462
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropilin-2 | protein | 554 | 3% helix, 46% strand | O60462 |
| H | Antibody heavy chain | protein | 222 | 7% helix, 50% strand | — |
| L | Antibody light chain | protein | 214 | 6% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.71 | 0.82 | 52 | empty |
| 2 | 951 | 0.70 | 0.75 | 88 | empty |
| 3 | 482 | 0.59 | 0.74 | 58 | empty |
| 4 | 294 | 0.57 | 0.77 | 35 | empty |
| 5 | 152 | 0.45 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2006 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 480 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 217 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 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 2QQL · PDBe 2QQL · UniProt O60462
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