MolNFT v1 · #142571 · protein
Crystal structure of bacterial protein toxins
6A8J · Rtx toxin: “Crystal structure of bacterial protein toxins”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #142571 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A8J
- 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
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rtx toxin | protein | 473 | 57% helix, 12% strand | — |
| B | Rtx toxin | protein | 472 | 57% helix, 11% strand | — |
| C, D | Rtx toxin | protein | 470 | 58% helix, 12% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.84 | 0.90 | 64 | empty |
| 2 | 538 | 0.84 | 0.90 | 68 | empty |
| 3 | 1116 | 0.76 | 0.78 | 115 | empty |
| 4 | 1104 | 0.75 | 0.78 | 108 | empty |
| 5 | 201 | 0.64 | 0.83 | 39 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1257 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1199 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6A8J · Crystal structure of 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 6A8J · PDBe 6A8J
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