Research workbench
Computationally designed thioredoxin DF106
Analyse Computationally designed thioredoxin DF106 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7D
- Type
- protein
- Length
- 813 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Designed thioredoxin DF106
- Ligands
- CU
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Designed thioredoxin DF106 | protein | 106 | 42% helix, 26% strand | — |
| G | Designed thioredoxin DF106 | protein | 72 | 22% helix, 32% strand | — |
| H | Designed thioredoxin DF106 | protein | 105 | 41% helix, 27% strand | — |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B, D, F, C, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.65 | 0.80 | 57 | empty |
| 2 | 141 | 0.60 | 0.84 | 24 | empty |
| 3 | 216 | 0.55 | 0.78 | 42 | empty |
| 4 | 55 | 0.50 | 0.86 | 17 | empty |
| 5 | 51 | 0.48 | 0.86 | 15 | empty |
Interfaces
16 interfaces between chains.
- C–E · 637 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 627 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 615 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 607 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J7D · Computationally Designed Thioredoxin dF106 · 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 5J7D · PDBe 5J7D
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