MolNFT v1 · #137064 · protein
The crystal structure of der P 1 allergen complexed with Fab fragment of mab 10B9
5VCO · Light chain of Fab fragment of 10B9 antibody: “The crystal structure of der P 1 allergen complexed with Fab fragment of mab 10B9”. X-ray diffraction, 2 ligands (NAG, CA), 9 pockets (best druggability 0.60). MolNFT v1 #137064 on…
- PDB
- 5VCO
- Type
- protein
- Length
- 1,300 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab fragment of 10B9 antibody; Heavy chain of Fab fragment of 10B9…
- UniProt
- Q3HWZ5
- Ligands
- NAG, CA
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Light chain of Fab fragment of 10B9 antibody | protein | 211 | 6% helix, 51% strand | — |
| B | Heavy chain of Fab fragment of 10B9 antibody | protein | 215 | 8% helix, 52% strand | — |
| D | Heavy chain of Fab fragment of 10B9 antibody | protein | 219 | 11% helix, 53% strand | — |
| E, F | Peptidase 1 | protein | 222 | 28% helix, 22% strand | Q3HWZ5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, F
- CA · Calcium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.60 | 0.74 | 65 | empty |
| 2 | 477 | 0.58 | 0.73 | 53 | empty |
| 3 | 447 | 0.56 | 0.73 | 45 | empty |
| 4 | 69 | 0.47 | 0.83 | 20 | empty |
| 5 | 103 | 0.42 | 0.77 | 16 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1820 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 673 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 662 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 271 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VCO · The crystal structure of der P 1 allergen complexed with Fab fragment of mab 10B9 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3HWZ5
- Elsewhere: RCSB PDB 5VCO · PDBe 5VCO · UniProt Q3HWZ5
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