Research workbench
Ebola virus VP35 bound to small molecule
Analyse Ebola virus VP35 bound to small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IBJ
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35
- UniProt
- Q05127
- Ligands
- 1D9
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Polymerase cofactor VP35 | protein | 124 | 52% helix, 15% strand | Q05127 |
Ligands and binding sites
- 1D9 · 3-{(5S)-3-hydroxy-2-oxo-4-[3-(trifluoromethyl)benzoyl]-5-[3-(trifluoromethyl)phenyl]-2,5-dihydro-1H-pyrrol-1-yl}benzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.71 | 0.76 | 70 | 1D9 |
Interfaces
1 interface between chains.
- A–B · 255 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4IBJ · Ebola virus VP35 bound to small molecule · 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 4IBJ · PDBe 4IBJ · UniProt Q05127
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