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Crystal structure of the virus like particle of flock house virus
Analyse Crystal structure of the virus like particle 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
- 4FSJ
- Type
- protein + RNA
- Length
- 1,001 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein beta; Capsid protein gamma; Random cellular RNA fragments
- EC
- 3.4.23.44
- UniProt
- P12870
- Ligands
- CA, CL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein beta (EC 3.4.23.44) | protein | 315 | 16% helix, 39% strand | P12870 |
| D | Capsid protein gamma | protein | 18 | 61% helix, 0% strand | P12870 |
| B, C | Capsid protein beta (EC 3.4.23.44) | protein | 309 | 14% helix, 39% strand | P12870 |
| E | Capsid protein gamma | protein | 17 | 59% helix, 0% strand | P12870 |
| F | Capsid protein gamma | protein | 19 | 79% helix, 0% strand | P12870 |
| R | Random cellular RNA fragments | rna | 14 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, C, B
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.85 | 0.86 | 58 | empty |
| 2 | 180 | 0.77 | 0.93 | 31 | empty |
| 3 | 287 | 0.77 | 0.89 | 32 | empty |
| 4 | 302 | 0.77 | 0.89 | 32 | empty |
| 5 | 77 | 0.76 | 0.98 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1934 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1743 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1733 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 754 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 734 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4FSJ · Crystal structure of the virus like particle of Flock House virus · the same entry in another collection · chain B against B, 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 4FSJ · PDBe 4FSJ · UniProt P12870
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