Research workbench
Crystal structure of the D75N mutant capsid of flock house virus
Analyse Crystal structure of the D75N mutant capsid of flock house virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FTE
- Type
- protein + RNA
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein alpha; Random cellular rnas
- EC
- 3.4.23.44
- UniProt
- P12870
- Ligands
- CA, SO4, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein alpha (EC 3.4.23.44) | protein | 328 | 21% helix, 38% strand | P12870 |
| B | Capsid protein alpha (EC 3.4.23.44) | protein | 330 | 21% helix, 37% strand | P12870 |
| C | Capsid protein alpha (EC 3.4.23.44) | protein | 329 | 20% helix, 37% strand | P12870 |
| R | Random cellular rnas | rna | 15 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B, C
- CL · Chloride ion · ion · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.86 | 0.87 | 53 | empty |
| 2 | 175 | 0.80 | 0.95 | 29 | empty |
| 3 | 265 | 0.76 | 0.89 | 29 | empty |
| 4 | 267 | 0.76 | 0.89 | 32 | empty |
| 5 | 268 | 0.75 | 0.89 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1746 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1745 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1727 Ų buried · 31 hydrogen bonds · protein-protein
- C–R · 255 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–R · 10 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4FTE · Crystal structure of the D75N mutant capsid of Flock House virus · 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 P12870
- Elsewhere: RCSB PDB 4FTE · PDBe 4FTE · UniProt P12870
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