MolNFT v1 · #27278 · protein
Crystal structure of the vibrio cholerae cytolysin (hlya) pro-toxin with octylglucoside bound
1XEZ · Hemolysin: “Crystal structure of the vibrio cholerae cytolysin (hlya) pro-toxin with octylglucoside bound”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #27278 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1XEZ
- Type
- protein
- Length
- 663 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemolysin
- UniProt
- P09545
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemolysin | protein | 663 | 8% helix, 49% strand | P09545 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.75 | 0.78 | 85 | empty |
| 2 | 58 | 0.56 | 0.88 | 16 | empty |
| 3 | 134 | 0.50 | 0.80 | 23 | empty |
| 4 | 160 | 0.47 | 0.77 | 25 | empty |
| 5 | 135 | 0.41 | 0.75 | 25 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1XEZ · Crystal Structure Of The Vibrio Cholerae Cytolysin (HlyA) Pro-Toxin With Octylglucoside… · the same entry in another collection · chain A against A, TM-score 1.00
- P09545 · AlphaFold monomer V2.0 prediction for hemolysin (P09545) · a predicted model of the same protein · 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 P09545
- Elsewhere: RCSB PDB 1XEZ · PDBe 1XEZ · UniProt P09545
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