Research workbench
Crystal structure of the virion-associated protein P3 from caulimovirus
Analyse Crystal structure of the virion-associated protein P3 from caulimovirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K4T
- Type
- protein
- Length
- 282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion-associated protein
- UniProt
- P03551
- Ligands
- CL
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virion-associated protein | protein | 70 | 86% helix, 0% strand | P03551 |
| B | Virion-associated protein | protein | 71 | 83% helix, 0% strand | P03551 |
| C | Virion-associated protein | protein | 73 | 77% helix, 0% strand | P03551 |
| D | Virion-associated protein | protein | 68 | 85% helix, 0% strand | P03551 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.84 | 0.98 | 26 | empty |
| 2 | 139 | 0.63 | 0.86 | 22 | CL |
Interfaces
6 interfaces between chains.
- A–C · 1714 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1674 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1631 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1561 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 274 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3K4T · Crystal structure of the virion-associated protein P3 from caulimovirus · 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 P03551
- Elsewhere: RCSB PDB 3K4T · PDBe 3K4T · UniProt P03551
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