Research workbench
The discobody: an engineered discoidin domain from factor VIII that binds V 3 integrin with antibody-like affinities
Analyse The discobody: an engineered discoidin domain from factor VIII that binds V 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PT6
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VIII
- UniProt
- P00451
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII | protein | 154 | 2% helix, 53% strand | P00451 |
| B | Coagulation factor VIII | protein | 153 | 2% helix, 50% strand | P00451 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.65 | 0.88 | 24 | empty |
| 2 | 116 | 0.48 | 0.80 | 26 | empty |
| 3 | 166 | 0.41 | 0.73 | 22 | empty |
| 4 | 85 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4PT6 · The discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin… · the same entry in another collection · chain A against A, TM-score 1.00
- P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P00451
- Elsewhere: RCSB PDB 4PT6 · PDBe 4PT6 · UniProt P00451
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