Research workbench
The crystal structure of a zinc finger - RNA complex reveals two modes of molecular recognition
Analyse The crystal structure of a zinc finger - RNA complex reveals two modes of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UN6
- Type
- protein + RNA
- Length
- 353 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor iiia; 5S ribosomal RNA
- UniProt
- P03001
- Ligands
- MG, ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transcription factor iiia | protein | 86 | 35% helix, 14% strand | P03001 |
| C | Transcription factor iiia | protein | 87 | 33% helix, 11% strand | P03001 |
| D | Transcription factor iiia | protein | 58 | 29% helix, 10% strand | P03001 |
| E, F | 5S ribosomal RNA | rna | 61 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 13 copies · chains B, E, C, F, D
- ZN · Zinc ion · metal · 8 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.79 | 0.81 | 65 | MG |
| 2 | 656 | 0.68 | 0.77 | 34 | empty |
| 3 | 316 | 0.52 | 0.74 | 34 | MG |
| 4 | 85 | 0.35 | 0.76 | 12 | empty |
| 5 | 104 | 0.35 | 0.74 | 16 | MG |
Interfaces
6 interfaces between chains.
- C–E · 917 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–F · 904 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–D · 813 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 284 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–F · 161 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 1UN6 · The crystal structure of a zinc finger - RNA complex reveals two modes of molecular… · the same entry in another collection · chain F against F, TM-score 1.00
- P03001 · AlphaFold monomer V2.0 prediction for transcription factor iiia (P03001) · a predicted model of the same protein · chain C against A, TM-score 0.57
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 P03001
- Elsewhere: RCSB PDB 1UN6 · PDBe 1UN6 · UniProt P03001
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