Research workbench
Crystal structure of a de novo designed protein with curved beta-sheet
Analyse Crystal structure of a de novo designed protein with curved beta-sheet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TS4
- Type
- protein
- Length
- 400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Denovo NTF2
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Denovo NTF2 | protein | 101 | 33% helix, 43% strand | — |
| B | Denovo NTF2 | protein | 106 | 29% helix, 45% strand | — |
| C | Denovo NTF2 | protein | 104 | 29% helix, 47% strand | — |
| D | Denovo NTF2 | protein | 89 | 26% helix, 40% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.72 | 0.78 | 78 | empty |
| 2 | 356 | 0.64 | 0.79 | 34 | empty |
| 3 | 167 | 0.52 | 0.79 | 28 | empty |
| 4 | 74 | 0.51 | 0.84 | 22 | PEG |
| 5 | 89 | 0.48 | 0.81 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 454 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5TS4 · Crystal structure of a de novo designed protein with curved beta-sheet · 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 5TS4 · PDBe 5TS4
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