MolNFT v1 · #142543 · protein
Bacterial protein toxins
6A7H · Rtx toxin: “Bacterial protein toxins”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.85). MolNFT v1 #142543 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A7H
- Type
- protein
- Length
- 1,885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rtx toxin
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rtx toxin | protein | 477 | 60% helix, 12% strand | — |
| B | Rtx toxin | protein | 471 | 60% helix, 11% strand | — |
| C | Rtx toxin | protein | 469 | 60% helix, 12% strand | — |
| D | Rtx toxin | protein | 468 | 60% helix, 12% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.85 | 0.90 | 69 | empty |
| 2 | 663 | 0.83 | 0.88 | 65 | empty |
| 3 | 973 | 0.75 | 0.78 | 88 | empty |
| 4 | 690 | 0.71 | 0.78 | 73 | empty |
| 5 | 221 | 0.67 | 0.84 | 43 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1142 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1118 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 427 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 221 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6A7H · Bacterial protein toxins · 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
- Elsewhere: RCSB PDB 6A7H · PDBe 6A7H
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