Research workbench
De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
Analyse De novo design of protein homo-oligomers with modular hydrogen bond… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J73
- Type
- protein
- Length
- 297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein design 2L4HC2_9
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein design 2L4HC2_9 | protein | 75 | 88% helix, 0% strand | — |
| C | Protein design 2L4HC2_9 | protein | 74 | 88% helix, 0% strand | — |
| D | Protein design 2L4HC2_9 | protein | 73 | 90% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.68 | 0.78 | 60 | empty |
| 2 | 142 | 0.57 | 0.83 | 26 | empty |
| 3 | 127 | 0.45 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1679 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1548 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 240 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5J73 · De novo design of protein homo-oligomers with modular hydrogen bond network-mediated… · 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 5J73 · PDBe 5J73
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