Research workbench
A new topology of the HK97-like fold revealed in bordetella bacteriophage: non-covalent chainmail secured by jellyrolls
Analyse A new topology of the HK97-like fold revealed in bordetella bacteriophage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J4U
- Type
- protein
- Length
- 3,254 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein; Cementing protein
- UniProt
- Q775C7, Q775C8
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Major capsid protein | protein | 327 | 23% helix, 22% strand | Q775C7 |
| G | Major capsid protein | protein | 312 | 21% helix, 23% strand | Q775C7 |
| H, I, J, K, L, M, N | Cementing protein | protein | 140 | 3% helix, 31% strand | Q775C8 |
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 | 944 | 0.75 | 0.78 | 102 | empty |
| 2 | 65 | 0.68 | 0.95 | 24 | empty |
| 3 | 487 | 0.68 | 0.79 | 53 | empty |
| 4 | 274 | 0.68 | 0.83 | 44 | empty |
| 5 | 55 | 0.66 | 0.95 | 22 | empty |
Interfaces
31 interfaces between chains.
- E–F · 2544 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 2540 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2537 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2506 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2498 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3J4U · A new topology of the HK97-like fold revealed in Bordetella bacteriophage: non-covalent… · 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 Q775C7
- Every structure of UniProt Q775C8
- Elsewhere: RCSB PDB 3J4U · PDBe 3J4U · UniProt Q775C7 · UniProt Q775C8
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