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An enumerative algorithm for de novo design of proteins with diverse pocket structures
Analyse An enumerative algorithm for de novo design of proteins with diverse pocket… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W40
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Denovo NTF2
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Denovo NTF2 | protein | 120 | 33% helix, 48% strand | — |
| B | Denovo NTF2 | protein | 115 | 27% helix, 57% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.83 | 0.97 | 25 | empty |
| 2 | 147 | 0.44 | 0.76 | 23 | empty |
| 3 | 55 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1041 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6W40 · An enumerative algorithm for de novo design of proteins with diverse pocket structures · 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
- Elsewhere: RCSB PDB 6W40 · PDBe 6W40
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