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
- 5U35
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- De novo NTF2 with large cavity
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | De novo NTF2 with large cavity | protein | 125 | 38% helix, 45% strand | — |
| B | De novo NTF2 with large cavity | protein | 121 | 38% helix, 46% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MXE · 2-methoxyethanol · additive · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.80 | 0.93 | 29 | PG4 |
| 2 | 231 | 0.78 | 0.91 | 30 | PG6 |
| 3 | 139 | 0.47 | 0.78 | 21 | empty |
| 4 | 149 | 0.44 | 0.76 | 26 | empty |
| 5 | 80 | 0.44 | 0.81 | 18 | NA |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5U35 · 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 5U35 · PDBe 5U35
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