Research workbench
Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of pasteurella multocida toxin
Analyse Crystal structures reveal a thiol-protease like catalytic triad in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EBF
- Type
- protein
- Length
- 711 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dermonecrotic toxin
- UniProt
- P17452
- Ligands
- 2PO, GLC
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Dermonecrotic toxin | protein | 711 | 46% helix, 13% strand | P17452 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.59 | 0.85 | 24 | empty |
| 2 | 217 | 0.55 | 0.78 | 34 | empty |
| 3 | 175 | 0.50 | 0.77 | 23 | empty |
| 4 | 148 | 0.48 | 0.77 | 36 | empty |
| 5 | 87 | 0.45 | 0.81 | 20 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2EBF · Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region… · the same entry in another collection · chain X against X, TM-score 1.00
- P17452 · AlphaFold monomer V2.0 prediction for dermonecrotic toxin (P17452) · a predicted model of the same protein · chain X 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 P17452
- Elsewhere: RCSB PDB 2EBF · PDBe 2EBF · UniProt P17452
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