Research workbench
Crystal structure of der P 1 complexed with Fab 4C1
Analyse Crystal structure of der P 1 complexed with Fab 4C1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPG
- Type
- protein
- Length
- 651 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Der P 1 allergen; Fab 4C1 - light chain; Fab 4C1 - heavy chain
- UniProt
- Q3HWZ5
- Ligands
- NAG, CA
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Der P 1 allergen | protein | 222 | 28% helix, 25% strand | Q3HWZ5 |
| C | Fab 4C1 - light chain | protein | 211 | 6% helix, 54% strand | — |
| D | Fab 4C1 - heavy chain | protein | 218 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.61 | 0.74 | 55 | empty |
| 2 | 261 | 0.60 | 0.79 | 37 | EDO |
| 3 | 56 | 0.50 | 0.87 | 20 | empty |
| 4 | 151 | 0.42 | 0.74 | 25 | empty |
| 5 | 106 | 0.36 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2015 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5VPG · Crystal structure of der P 1 complexed with Fab 4C1 · 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 5VPG · PDBe 5VPG · UniProt Q3HWZ5
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