Research workbench
Crystal structure of HK97 prohead II
Analyse Crystal structure of HK97 prohead II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8K
- Type
- protein
- Length
- 1,758 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P49861
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein | protein | 256 | 22% helix, 31% strand | P49861 |
| B | Major capsid protein | protein | 250 | 29% helix, 28% strand | P49861 |
| C, F | Major capsid protein | protein | 248 | 29% helix, 29% strand | P49861 |
| D | Major capsid protein | protein | 254 | 25% helix, 29% strand | P49861 |
| E | Major capsid protein | protein | 255 | 26% helix, 23% strand | P49861 |
| G | Major capsid protein | protein | 247 | 24% helix, 30% strand | P49861 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.73 | 0.78 | 79 | empty |
| 2 | 452 | 0.72 | 0.82 | 88 | empty |
| 3 | 431 | 0.70 | 0.81 | 53 | empty |
| 4 | 504 | 0.69 | 0.79 | 56 | empty |
| 5 | 420 | 0.67 | 0.79 | 38 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1576 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1519 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1472 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1405 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1196 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3E8K · Crystal structure of HK97 Prohead II · 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 P49861
- Elsewhere: RCSB PDB 3E8K · PDBe 3E8K · UniProt P49861
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