Research workbench
First crystal structure of E.COLI based recombinant diphtheria toxin mutant CRM197
Analyse First crystal structure of E.COLI based recombinant diphtheria toxin mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I82
- Type
- protein
- Length
- 2,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphtheria toxin
- UniProt
- Q5PY51
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphtheria toxin | protein | 509 | 35% helix, 27% strand | Q5PY51 |
| B | Diphtheria toxin | protein | 510 | 34% helix, 28% strand | Q5PY51 |
| C | Diphtheria toxin | protein | 514 | 35% helix, 28% strand | Q5PY51 |
| D | Diphtheria toxin | protein | 507 | 35% helix, 27% strand | Q5PY51 |
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 | 714 | 0.76 | 0.81 | 110 | empty |
| 2 | 726 | 0.71 | 0.77 | 81 | GOL |
| 3 | 559 | 0.67 | 0.77 | 59 | empty |
| 4 | 641 | 0.67 | 0.76 | 66 | empty |
| 5 | 108 | 0.67 | 0.90 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3927 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3893 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5I82 · First Crystal Structure of E.coli Based Recombinant Diphtheria Toxin Mutant CRM197 · 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 Q5PY51
- Elsewhere: RCSB PDB 5I82 · PDBe 5I82 · UniProt Q5PY51
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