Research workbench
Crystal structure of EVP30 C-terminus and enp peptide
Analyse Crystal structure of EVP30 C-terminus and enp peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VAO
- Type
- protein
- Length
- 558 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Minor nucleoprotein VP30; Np
- UniProt
- Q77DJ5, A0A0D5W865
- Ligands
- CA, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minor nucleoprotein VP30 | protein | 127 | 70% helix, 0% strand | Q77DJ5 |
| B, C, D | Minor nucleoprotein VP30 | protein | 129 | 69% helix, 0% strand | Q77DJ5 |
| E, F, G, H | Np | protein | 11 | 0% helix, 0% strand | A0A0D5W865 |
Ligands and binding sites
- CA · Calcium ion · metal · chains D
- CL · Chloride ion · ion · 8 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, C, D, E, G
- GOL · Glycerol · additive · 4 copies · chains B, C, D
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 | 777 | 0.78 | 0.82 | 81 | GOL, PEG |
| 2 | 170 | 0.50 | 0.78 | 30 | empty |
| 3 | 123 | 0.43 | 0.77 | 20 | empty |
| 4 | 50 | 0.30 | 0.76 | 18 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1854 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 690 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 660 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 643 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 609 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VAO · Crystal structure of eVP30 C-terminus and eNP peptide · 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 Q77DJ5
- Every structure of UniProt A0A0D5W865
- Elsewhere: RCSB PDB 5VAO · PDBe 5VAO · UniProt Q77DJ5 · UniProt A0A0D5W865
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