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Crystal structure demonstrating ctd-ctd interactions of zaire ebola virus VP40 dimer
Analyse Crystal structure demonstrating ctd-ctd interactions of zaire ebola virus VP40… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZJ
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix protein VP40
- UniProt
- Q05128
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix protein VP40 | protein | 249 | 18% helix, 37% strand | Q05128 |
| B | Matrix protein VP40 | protein | 267 | 17% helix, 36% strand | Q05128 |
| C | Matrix protein VP40 | protein | 240 | 16% helix, 36% strand | Q05128 |
| D | Matrix protein VP40 | protein | 246 | 15% helix, 37% strand | Q05128 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.87 | 0.88 | 107 | 1PE |
| 2 | 1047 | 0.85 | 0.86 | 99 | empty |
| 3 | 101 | 0.55 | 0.85 | 32 | empty |
| 4 | 97 | 0.49 | 0.82 | 34 | empty |
| 5 | 98 | 0.48 | 0.81 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–D · 807 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 806 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7JZJ · Crystal structure demonstrating CTD-CTD interactions of Zaire Ebola virus VP40 dimer · 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 Q05128
- Elsewhere: RCSB PDB 7JZJ · PDBe 7JZJ · UniProt Q05128
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