Research workbench
Crystal structure of complex between recombinant der P 2.0103 and Fab fragment of 7A1
Analyse Crystal structure of complex between recombinant der P 2.0103 and Fab fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OY4
- Type
- protein
- Length
- 555 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Der P 2 variant 3; Fab fragment of IgG, light chain; Fab fragment of IgG, heavy chain
- UniProt
- I2CMD6
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Der P 2 variant 3 | protein | 122 | 2% helix, 48% strand | I2CMD6 |
| C | Fab fragment of IgG, light chain | protein | 216 | 6% helix, 56% strand | — |
| D | Fab fragment of IgG, heavy chain | protein | 217 | 12% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.83 | 0.90 | 59 | empty |
| 2 | 307 | 0.53 | 0.75 | 45 | empty |
| 3 | 79 | 0.48 | 0.83 | 23 | empty |
| 4 | 96 | 0.37 | 0.75 | 21 | empty |
| 5 | 106 | 0.36 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1790 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6OY4 · Crystal structure of complex between recombinant Der p 2.0103 and Fab fragment of 7A1 · 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 I2CMD6
- Elsewhere: RCSB PDB 6OY4 · PDBe 6OY4 · UniProt I2CMD6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.