Research workbench
Anthrax octamer prechannel bound to full-length lethal factor
Analyse Anthrax octamer prechannel bound to full-length lethal factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJJ
- Type
- protein
- Length
- 7,076 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protective antigen; Lethal factor
- UniProt
- P13423, I3XID8
- Ligands
- CA, ZN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Protective antigen | protein | 523 | 15% helix, 31% strand | P13423 |
| B, F, G, H | Protective antigen | protein | 523 | 16% helix, 32% strand | P13423 |
| L, I, J, K | Lethal factor | protein | 723 | 48% helix, 11% strand | I3XID8 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, F, D, G, E, H
- ZN · Zinc ion · metal · 4 copies · chains L, I, J, K
- SO4 · Sulfate ion · ion · 4 copies · chains L, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.81 | 0.84 | 88 | empty |
| 2 | 637 | 0.80 | 0.85 | 77 | empty |
| 3 | 864 | 0.80 | 0.83 | 84 | empty |
| 4 | 631 | 0.80 | 0.85 | 78 | empty |
| 5 | 1186 | 0.80 | 0.81 | 121 | empty |
Interfaces
20 interfaces between chains.
- F–D · 1551 Ų buried · 17 hydrogen bonds · protein-protein
- G–E · 1548 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 1543 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 1537 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6WJJ · Anthrax octamer prechannel bound to full-length lethal factor · the same entry in another collection · chain K against K, 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 P13423
- Every structure of UniProt I3XID8
- Elsewhere: RCSB PDB 6WJJ · PDBe 6WJJ · UniProt P13423 · UniProt I3XID8
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