MolNFT v1 · #118601 · protein
De novo design and crystallographic validation of antibodies targeting a pre-selected epitope
5F72 · Kelch-like ech-associated protein 1: “De novo design and crystallographic validation of antibodies targeting a pre-selected epitope”. X-ray diffraction, 7 pockets (best druggability 0.84). MolNFT v1 #118601 on GenesisL1: 3D…
- PDB
- 5F72
- Type
- protein
- Length
- 1,025 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch-like ech-associated protein 1; Single chain fv from a Fab
- UniProt
- Q14145
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, C | Kelch-like ech-associated protein 1 | protein | 285 | 0% helix, 50% strand | Q14145 |
| T | Single chain fv from a Fab | protein | 229 | 4% helix, 52% strand | — |
| S | Single chain fv from a Fab | protein | 226 | 3% helix, 52% strand | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.84 | 0.87 | 76 | empty |
| 2 | 897 | 0.83 | 0.85 | 92 | empty |
| 3 | 604 | 0.77 | 0.83 | 70 | empty |
| 4 | 157 | 0.50 | 0.78 | 30 | empty |
| 5 | 131 | 0.42 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–T · 1101 Ų buried · 25 hydrogen bonds · protein-protein
- K–S · 1085 Ų buried · 21 hydrogen bonds · protein-protein
- K–C · 388 Ų buried · 2 hydrogen bonds · protein-protein
- K–T · 351 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5F72 · De novo design and crystallographic validation of antibodies targeting a pre-selected… · the same entry in another collection · chain K against K, 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 Q14145
- Elsewhere: RCSB PDB 5F72 · PDBe 5F72 · UniProt Q14145
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