Research workbench
Crystal structure of reston ebolavirus VP35 RNA binding domain in complex with 18BP dsrna
Analyse Crystal structure of reston ebolavirus VP35 RNA binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KS8
- Type
- protein + RNA
- Length
- 528 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A) -3'…
- UniProt
- Q8JPY0
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-R(*AP*GP*AP*AP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*A) -3' | rna | 18 | — | — |
| F | 5'-R(*UP*CP*CP*UP*CP*CP*CP*UP*CP*CP*CP*UP*CP*CP*UP*UP*CP*U) -3' | rna | 18 | — | — |
| A, C | Polymerase cofactor VP35 | protein | 122 | 53% helix, 13% strand | Q8JPY0 |
| B, D | Polymerase cofactor VP35 | protein | 124 | 54% helix, 13% strand | Q8JPY0 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.63 | 0.91 | 23 | empty |
| 2 | 82 | 0.62 | 0.90 | 23 | empty |
| 3 | 219 | 0.57 | 0.79 | 35 | empty |
| 4 | 225 | 0.56 | 0.79 | 35 | empty |
| 5 | 88 | 0.34 | 0.75 | 16 | empty |
Interfaces
11 interfaces between chains.
- E–F · 880 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- A–B · 362 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 358 Ų buried · 13 hydrogen bonds · protein-protein
- E–C · 298 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–A · 287 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3KS8 · Crystal structure of Reston ebolavirus VP35 RNA binding domain in complex with 18bp dsRNA · the same entry in another collection · chain E against E, 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 Q8JPY0
- Elsewhere: RCSB PDB 3KS8 · PDBe 3KS8 · UniProt Q8JPY0
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