Research workbench
Bacteriophage PRD1 major capsid protein P3 in complex with cpz
Analyse Bacteriophage PRD1 major capsid protein P3 in complex with cpz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OOK
- Type
- protein
- Length
- 1,119 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein P3
- UniProt
- P22535
- Ligands
- Z80, NA, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A | Major capsid protein P3 | protein | 373 | 15% helix, 42% strand | P22535 |
Ligands and binding sites
- Z80 · 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine · ligand · 3 copies · chains C, B, A
- NA · Sodium ion · metal · 5 copies · chains C, B, A
- CL · Chloride ion · ion · 3 copies · chains B, A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.78 | 0.84 | 50 | Z80 |
| 2 | 855 | 0.78 | 0.81 | 84 | Z80 |
| 3 | 611 | 0.78 | 0.83 | 51 | Z80 |
| 4 | 91 | 0.33 | 0.73 | 23 | MPD |
| 5 | 60 | 0.26 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1744 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 1729 Ų buried · 34 hydrogen bonds · protein-protein
- C–A · 1728 Ų buried · 35 hydrogen bonds · protein-protein
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 P22535
- Elsewhere: RCSB PDB 7OOK · PDBe 7OOK · UniProt P22535
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.