Research workbench
Structure of the major structural protein D135 of acidianus tailed spindle virus (atsv)
Analyse Structure of the major structural protein D135 of acidianus tailed spindle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQW
- Type
- protein
- Length
- 612 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative major coat protein
- UniProt
- A0A125SJ78
- Ligands
- NO3
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Putative major coat protein | protein | 122 | 64% helix, 4% strand | A0A125SJ78 |
| B, E | Putative major coat protein | protein | 123 | 67% helix, 4% strand | A0A125SJ78 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.48 | 0.77 | 23 | empty |
| 2 | 147 | 0.46 | 0.76 | 21 | empty |
| 3 | 161 | 0.45 | 0.75 | 22 | empty |
| 4 | 139 | 0.45 | 0.76 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 746 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 729 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 729 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 728 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 5EQW · Structure of the major structural protein D135 of Acidianus tailed spindle virus (ATSV) · 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 A0A125SJ78
- Elsewhere: RCSB PDB 5EQW · PDBe 5EQW · UniProt A0A125SJ78
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