Research workbench
Crystal structure of human SND1 extended tudor domain in complex with a symmetrically dimethylated E2F peptide
Analyse Crystal structure of human SND1 extended tudor domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M9O
- Type
- protein
- Length
- 220 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylococcal nuclease domain-containing protein 1; E2F peptide
- UniProt
- Q7KZF4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal nuclease domain-containing protein 1 | protein | 216 | 32% helix, 31% strand | Q7KZF4 |
| B | E2F peptide | protein | 4 | 0% helix, 0% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.38 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 413 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5M9O · Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7KZF4 · AlphaFold monomer V2.0 prediction for staphylococcal nuclease domain- containing protein… · a predicted model of the same protein · chain A 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 Q7KZF4
- Elsewhere: RCSB PDB 5M9O · PDBe 5M9O · UniProt Q7KZF4
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