Research workbench
PUF3 RNA binding domain bound to COX17 RNA 3' utr recognition sequence site B
Analyse PUF3 RNA binding domain bound to COX17 RNA 3' utr recognition sequence site B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K49
- Type
- protein + RNA
- Length
- 1,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-binding protein PUF3; RNA (5'-R(*CP*CP*UP*GP*UP*AP*AP*AP*UP*A)-3')
- UniProt
- Q07807
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | MRNA-binding protein PUF3 | protein | 353 | 72% helix, 0% strand | Q07807 |
| B, D, F | RNA (5'-R(*CP*CP*UP*GP*UP*AP*AP*AP*UP*A)-3') | rna | 10 | — | — |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.64 | 0.77 | 55 | empty |
| 2 | 428 | 0.62 | 0.77 | 45 | empty |
| 3 | 335 | 0.60 | 0.78 | 31 | empty |
| 4 | 128 | 0.37 | 0.73 | 19 | empty |
| 5 | 75 | 0.35 | 0.76 | 15 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1562 Ų buried · 62 hydrogen bonds · protein-nucleic
- A–B · 1559 Ų buried · 60 hydrogen bonds · protein-nucleic
- E–F · 1553 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–C · 309 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 296 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3K49 · Puf3 RNA binding domain bound to Cox17 RNA 3' UTR recognition sequence site B · the same entry in another collection · chain C against C, TM-score 1.00
- Q07807 · AlphaFold monomer V2.0 prediction for mRNA-binding protein PUF3 (Q07807) · a predicted model of the same protein · chain A 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 Q07807
- Elsewhere: RCSB PDB 3K49 · PDBe 3K49 · UniProt Q07807
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