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Crystal structure of a ternary complex of fbf-2 with lst-1 (site B) and compact fbe RNA
Analyse Crystal structure of a ternary complex of fbf-2 with lst-1 (site B) and compact… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PUN
- Type
- protein + RNA
- Length
- 830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fem-3 mRNA-binding factor 2; RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3'); Lst-1
- UniProt
- Q09312, Q86RT0
- Ligands
- NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fem-3 mRNA-binding factor 2 | protein | 396 | 72% helix, 2% strand | Q09312 |
| B | RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3') | rna | 8 | — | — |
| C | Fem-3 mRNA-binding factor 2 | protein | 388 | 72% helix, 1% strand | Q09312 |
| D | RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3') | rna | 7 | — | — |
| E | Lst-1 | protein | 15 | 0% helix, 13% strand | Q86RT0 |
| F | Lst-1 | protein | 16 | 0% helix, 13% strand | Q86RT0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.73 | 0.77 | 109 | empty |
| 2 | 99 | 0.37 | 0.75 | 25 | empty |
| 3 | 73 | 0.30 | 0.74 | 19 | EDO |
| 4 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1310 Ų buried · 45 hydrogen bonds · protein-nucleic
- C–D · 1308 Ų buried · 49 hydrogen bonds · protein-nucleic
- A–E · 880 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 860 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 833 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6PUN · Crystal structure of a ternary complex of FBF-2 with LST-1 (site B) and compact FBE RNA · the same entry in another collection · chain F against F, TM-score 1.00
- Q09312 · AlphaFold monomer V2.0 prediction for fem-3 mRNA-binding factor 2 (Q09312) · a predicted model of the same protein · chain A 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 Q09312
- Every structure of UniProt Q86RT0
- Elsewhere: RCSB PDB 6PUN · PDBe 6PUN · UniProt Q09312 · UniProt Q86RT0
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