MolNFT v1 · #66608 · protein
The protective antigen component of anthrax toxin forms functional octameric complexes
3HVD: “The protective antigen component of anthrax toxin forms functional octameric complexes”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.79). MolNFT v1 #66608 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3HVD
- Type
- protein
- Length
- 4,150 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protective antigen
- UniProt
- Q08G54
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protective antigen | protein | 518 | 16% helix, 35% strand | Q08G54 |
| B | Protective antigen | protein | 523 | 18% helix, 32% strand | Q08G54 |
| C | Protective antigen | protein | 517 | 16% helix, 35% strand | Q08G54 |
| D, H | Protective antigen | protein | 518 | 19% helix, 33% strand | Q08G54 |
| E | Protective antigen | protein | 519 | 16% helix, 34% strand | Q08G54 |
| F | Protective antigen | protein | 519 | 18% helix, 33% strand | Q08G54 |
| G | Protective antigen | protein | 518 | 16% helix, 35% strand | Q08G54 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
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 | 806 | 0.79 | 0.82 | 125 | empty |
| 2 | 974 | 0.79 | 0.81 | 100 | empty |
| 3 | 976 | 0.78 | 0.80 | 100 | empty |
| 4 | 1186 | 0.78 | 0.80 | 132 | empty |
| 5 | 457 | 0.77 | 0.86 | 54 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1573 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1535 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1512 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1486 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3HVD · The Protective Antigen Component of Anthrax Toxin Forms Functional Octameric Complexes · 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 Q08G54
- Elsewhere: RCSB PDB 3HVD · PDBe 3HVD · UniProt Q08G54
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