MolNFT v1 · #74089 · protein
Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R14ME2S
3OMG · Staphylococcal nuclease domain-containing protein 1: “Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1…”. X-ray diffraction, 2 pockets (best druggability 0.70). MolNFT v1…
- 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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