Research workbench
Crystal structure of human schlafen 5 N'-terminal domain (SLFN5-N) involved in ssrna cleaving and DNA binding
Analyse Crystal structure of human schlafen 5 N'-terminal domain (SLFN5-N) involved in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CUX
- Type
- protein
- Length
- 1,764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Schlafen family member 5
- UniProt
- Q08AF3
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Schlafen family member 5 | protein | 292 | 31% helix, 29% strand | Q08AF3 |
| B, D, E | Schlafen family member 5 | protein | 295 | 31% helix, 30% strand | Q08AF3 |
| C | Schlafen family member 5 | protein | 291 | 31% helix, 28% strand | Q08AF3 |
| F | Schlafen family member 5 | protein | 296 | 31% helix, 30% strand | Q08AF3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.87 | 0.88 | 135 | empty |
| 2 | 223 | 0.79 | 0.92 | 39 | empty |
| 3 | 234 | 0.73 | 0.88 | 36 | empty |
| 4 | 264 | 0.72 | 0.86 | 43 | empty |
| 5 | 114 | 0.71 | 0.92 | 27 | empty |
Interfaces
12 interfaces between chains.
- A–E · 713 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 700 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 682 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 464 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7CUX · Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA… · the same entry in another collection · chain F against F, TM-score 1.00
- Q08AF3 · AlphaFold monomer V2.0 prediction for schlafen family member 5 (Q08AF3) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q08AF3
- Elsewhere: RCSB PDB 7CUX · PDBe 7CUX · UniProt Q08AF3
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