Research workbench
Crystal structure of human TDRD1 extended tudor domain in complex with a symmetrically dimethylated E2F peptide
Analyse Crystal structure of human TDRD1 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
- 5M9N
- Type
- protein
- Length
- 404 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tudor domain-containing protein 1; E2F peptide
- UniProt
- Q9BXT4
- Ligands
- 2MR
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tudor domain-containing protein 1 | protein | 202 | 23% helix, 38% strand | Q9BXT4 |
| B | Tudor domain-containing protein 1 | protein | 198 | 23% helix, 35% strand | Q9BXT4 |
| C | E2F peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2MR · N3, N4-dimethylarginine · ligand · chains B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.65 | 0.75 | 72 | EDO |
| 2 | 391 | 0.60 | 0.76 | 48 | empty |
| 3 | 187 | 0.52 | 0.77 | 30 | empty |
| 4 | 148 | 0.47 | 0.77 | 23 | empty |
| 5 | 63 | 0.38 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 684 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 5M9N · Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BXT4 · AlphaFold monomer V2.0 prediction for tudor domain-containing protein 1 (Q9BXT4) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9BXT4
- Elsewhere: RCSB PDB 5M9N · PDBe 5M9N · UniProt Q9BXT4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.