Research workbench
Crystal structure of de novo designed helical repeat protein DHR8
Analyse Crystal structure of de novo designed helical repeat protein DHR8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CWF
- Type
- protein
- Length
- 704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed helical repeat protein
- Ligands
- CA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Designed helical repeat protein | protein | 177 | 87% helix, 0% strand | — |
| B | Designed helical repeat protein | protein | 176 | 86% helix, 1% strand | — |
| C | Designed helical repeat protein | protein | 175 | 87% helix, 1% strand | — |
| D | Designed helical repeat protein | protein | 176 | 87% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 32 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.79 | 0.82 | 106 | CA |
| 2 | 114 | 0.78 | 0.97 | 21 | empty |
| 3 | 107 | 0.78 | 0.98 | 21 | empty |
| 4 | 55 | 0.66 | 0.96 | 14 | empty |
| 5 | 109 | 0.53 | 0.83 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1086 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1085 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 304 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 273 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5CWF · Crystal structure of de novo designed helical repeat protein DHR8 · 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 5CWF · PDBe 5CWF
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