Research workbench
Crystal structure of C. elegans puf-8 in complex with RNA
Analyse Crystal structure of C. elegans puf-8 in complex with RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NOD
- Type
- protein + RNA
- Length
- 1,056 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Puf (PUMILIO/FBF) domain-containing; RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')
- UniProt
- Q09487
- Pockets
- 14 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Puf (PUMILIO/FBF) domain-containing | protein | 344 | 75% helix, 1% strand | Q09487 |
| D, E, F | RNA (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3') | rna | 8 | — | — |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.55 | 0.79 | 27 | empty |
| 2 | 220 | 0.53 | 0.77 | 28 | empty |
| 3 | 194 | 0.52 | 0.77 | 24 | empty |
| 4 | 54 | 0.49 | 0.86 | 13 | empty |
| 5 | 163 | 0.49 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–F · 1231 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–E · 1220 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–D · 1209 Ų buried · 40 hydrogen bonds · protein-nucleic
- B–C · 839 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 810 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NOD · Crystal structure of C. elegans PUF-8 in complex with RNA · the same entry in another collection · chain A against A, TM-score 1.00
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 Q09487
- Elsewhere: RCSB PDB 6NOD · PDBe 6NOD · UniProt Q09487
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