Research workbench
Crystal structure of RNA polymerase-associated protein RTF1 homolog plus-3 domain
Analyse Crystal structure of RNA polymerase-associated protein RTF1 homolog plus-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U1U
- Type
- protein
- Length
- 260 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase-associated protein RTF1 homolog
- UniProt
- Q92541
- Ligands
- UNX, SO4
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase-associated protein RTF1 homolog | protein | 131 | 34% helix, 36% strand | Q92541 |
| B | RNA polymerase-associated protein RTF1 homolog | protein | 129 | 35% helix, 36% strand | Q92541 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 23 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.47 | 0.78 | 18 | SO4 |
| 2 | 85 | 0.35 | 0.75 | 19 | SO4, UNX |
| 3 | 54 | 0.29 | 0.75 | 15 | UNX |
Interfaces
1 interface between chains.
- A–B · 405 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3U1U · Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q92541 · AlphaFold monomer V2.0 prediction for RNA polymerase-associated protein RTF1 homolog… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q92541
- Elsewhere: RCSB PDB 3U1U · PDBe 3U1U · UniProt Q92541
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