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Crystal structure of zaire ebola VP35 interferon inhibitory domain bound to 8 bp dsrna
Analyse Crystal structure of zaire ebola VP35 interferon inhibitory domain bound to 8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L26
- Type
- protein + RNA
- Length
- 254 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35; RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
- UniProt
- Q05127
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polymerase cofactor VP35 | protein | 123 | 49% helix, 15% strand | Q05127 |
| C | RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3') | rna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.54 | 0.78 | 30 | empty |
| 2 | 139 | 0.41 | 0.75 | 17 | empty |
| 3 | 128 | 0.38 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 332 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 214 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3L26 · Crystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA · 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 Q05127
- Elsewhere: RCSB PDB 3L26 · PDBe 3L26 · UniProt Q05127
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