MolNFT v1 · #118067 · protein
Structure of the major structural protein D135 of acidianus tailed spindle virus (atsv)
5EQW · Putative major coat protein: “Structure of the major structural protein D135 of acidianus tailed spindle virus (atsv)”. X-ray diffraction, 1 ligand (NO3), 4 pockets (best druggability 0.48). MolNFT v1 #118067 on GenesisL1: 3D…
- 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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