Research workbench
The crystal structure of der P 1 allergen complexed with Fab fragment of mab 5H8
Analyse The crystal structure of der P 1 allergen complexed with Fab fragment of mab 5H8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCN
- Type
- protein
- Length
- 1,291 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase 1; Light chain of Fab fragment of mab 5H8; Heavy chain of Fab fragment of mab…
- UniProt
- Q3HWZ5
- Ligands
- NAG, CA, PO4
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidase 1 | protein | 222 | 29% helix, 23% strand | Q3HWZ5 |
| C, E | Light chain of Fab fragment of mab 5H8 | protein | 210 | 5% helix, 51% strand | — |
| D | Heavy chain of Fab fragment of mab 5H8 | protein | 213 | 3% helix, 51% strand | — |
| F | Heavy chain of Fab fragment of mab 5H8 | protein | 214 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.51 | 0.74 | 47 | empty |
| 2 | 133 | 0.41 | 0.75 | 26 | empty |
| 3 | 137 | 0.38 | 0.73 | 30 | empty |
| 4 | 53 | 0.32 | 0.77 | 14 | empty |
| 5 | 69 | 0.32 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1832 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1830 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 720 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 720 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 260 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VCN · The crystal structure of der P 1 allergen complexed with Fab fragment of mab 5H8 · 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 5VCN · PDBe 5VCN · UniProt Q3HWZ5
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