Research workbench
Crystal structure of the N363T mutant of the flock house virus capsid
Analyse Crystal structure of the N363T mutant of the flock house virus capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FTS
- Type
- protein + RNA
- Length
- 1,001 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, CL, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein alpha (EC 3.4.23.44) | protein | 328 | 21% helix, 37% strand | P12870 |
| B | Capsid protein alpha (EC 3.4.23.44) | protein | 329 | 19% helix, 37% strand | P12870 |
| C | Capsid protein alpha (EC 3.4.23.44) | protein | 329 | 18% helix, 36% strand | P12870 |
| R | Random cellular rnas | rna | 15 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- SO4 · Sulfate ion · ion · chains A, B, C
- 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
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.85 | 0.87 | 56 | empty |
| 2 | 192 | 0.82 | 0.96 | 36 | empty |
| 3 | 284 | 0.77 | 0.89 | 29 | empty |
| 4 | 290 | 0.77 | 0.89 | 28 | empty |
| 5 | 266 | 0.76 | 0.89 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1771 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1763 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1759 Ų buried · 26 hydrogen bonds · protein-protein
- C–R · 250 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–R · 89 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4FTS · Crystal structure of the N363T mutant of the Flock House virus capsid · 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 4FTS · PDBe 4FTS · UniProt P12870
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