Research workbench
Crystal structure of albireti toxin, a diphtheria toxin homolog, from streptomyces albireticuli
Analyse Crystal structure of albireti toxin, a diphtheria toxin homolog, from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RI3
- Type
- protein
- Length
- 2,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DIPHTHERIA_T domain-containing protein
- UniProt
- A0A2A2D7J4
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DIPHTHERIA_T domain-containing protein | protein | 572 | 34% helix, 23% strand | A0A2A2D7J4 |
| B | DIPHTHERIA_T domain-containing protein | protein | 575 | 33% helix, 24% strand | A0A2A2D7J4 |
| C | DIPHTHERIA_T domain-containing protein | protein | 583 | 34% helix, 22% strand | A0A2A2D7J4 |
| D | DIPHTHERIA_T domain-containing protein | protein | 578 | 34% helix, 23% strand | A0A2A2D7J4 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.82 | 0.88 | 70 | ACT |
| 2 | 693 | 0.81 | 0.85 | 69 | ACT |
| 3 | 666 | 0.79 | 0.84 | 75 | ACT |
| 4 | 613 | 0.79 | 0.84 | 70 | ACT |
| 5 | 653 | 0.75 | 0.82 | 77 | PG4 |
Interfaces
4 interfaces between chains.
- A–C · 612 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 533 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 456 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 349 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 8 disulfide (engineered, disulfide).
Compared structures
- 7RI3 · Crystal structure of Albireti Toxin, a diphtheria toxin homolog, from Streptomyces… · the same entry in another collection · chain B against B, 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 A0A2A2D7J4
- Elsewhere: RCSB PDB 7RI3 · PDBe 7RI3 · UniProt A0A2A2D7J4
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