Research workbench
Computationally designed tim-barrel protein, halfflr
Analyse Computationally designed tim-barrel protein, halfflr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TDM
- Type
- protein
- Length
- 471 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Computationally designed two-fold symmetric tim-barrel protein, flr (half molecule)
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Computationally designed two-fold symmetric tim-barrel protein, flr (half molecule) | protein | 120 | 38% helix, 30% strand | — |
| B, D | Computationally designed two-fold symmetric tim-barrel protein, flr (half molecule) | protein | 120 | 38% helix, 23% strand | — |
| C | Computationally designed two-fold symmetric tim-barrel protein, flr (half molecule) | protein | 111 | 26% helix, 30% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.74 | 0.87 | 47 | PO4 |
| 2 | 205 | 0.61 | 0.82 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1794 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 398 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3TDM · Computationally designed TIM-barrel protein, HalfFLR · 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 3TDM · PDBe 3TDM
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