Research workbench
Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R14ME2S
Analyse Structure of human SND1 extended tudor domain in complex with the symmetrically… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OMG
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylococcal nuclease domain-containing protein 1; Dimethylated arginine peptide R14ME2S
- UniProt
- Q7KZF4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal nuclease domain-containing protein 1 | protein | 213 | 33% helix, 31% strand | Q7KZF4 |
| B | Staphylococcal nuclease domain-containing protein 1 | protein | 216 | 34% helix, 31% strand | Q7KZF4 |
| C | Dimethylated arginine peptide R14ME2S | protein | 6 | 0% helix, 0% strand | — |
| D | Dimethylated arginine peptide R14ME2S | protein | 5 | 0% helix, 0% strand | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.70 | 0.76 | 58 | empty |
| 2 | 88 | 0.40 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 407 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3OMG · Structure of human SND1 extended tudor domain in complex with the 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 3OMG · PDBe 3OMG · UniProt Q7KZF4
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