Research workbench
Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49
Analyse Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NFI
- Type
- protein
- Length
- 1,092 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase I subunit RPA49
- EC
- 2.7.7.6
- UniProt
- Q01080
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 219 | 55% helix, 8% strand | Q01080 |
| B | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 227 | 56% helix, 7% strand | Q01080 |
| C | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 214 | 54% helix, 8% strand | Q01080 |
| D | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 220 | 53% helix, 8% strand | Q01080 |
| E | DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6) | protein | 212 | 54% helix, 5% strand | Q01080 |
Ligands and binding sites
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.71 | 0.77 | 74 | empty |
| 2 | 332 | 0.65 | 0.80 | 51 | empty |
| 3 | 320 | 0.60 | 0.78 | 36 | empty |
| 4 | 239 | 0.58 | 0.79 | 30 | empty |
| 5 | 313 | 0.53 | 0.74 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–B · 782 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 749 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 504 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3NFI · Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 · the same entry in another collection · chain E against E, TM-score 1.00
- Q01080 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase I subunit RPA49 (Q01080) · a predicted model of the same protein · chain E 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 Q01080
- Elsewhere: RCSB PDB 3NFI · PDBe 3NFI · UniProt Q01080
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