Research workbench
Crystal structure of the vibrio vulnificus HEMOLYSIN/CYTOLYSIN beta- trefoil lectin with N-acetyl-D-galactosamine bound
Analyse Crystal structure of the vibrio vulnificus HEMOLYSIN/CYTOLYSIN beta- trefoil… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OWK
- Type
- protein
- Length
- 924 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytolysin
- UniProt
- P19247
- Ligands
- NGA
- Pockets
- 8 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, G | Cytolysin | protein | 131 | 7% helix, 45% strand | P19247 |
| E | Cytolysin | protein | 136 | 7% helix, 44% strand | P19247 |
| F | Cytolysin | protein | 133 | 7% helix, 42% strand | P19247 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 7 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · 6 copies · chains A, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.34 | 0.77 | 15 | empty |
| 2 | 52 | 0.34 | 0.78 | 15 | empty |
| 3 | 59 | 0.32 | 0.76 | 16 | empty |
| 4 | 59 | 0.31 | 0.76 | 16 | empty |
| 5 | 58 | 0.29 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- E–F · 443 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 439 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 437 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 406 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 397 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4OWK · Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with… · the same entry in another collection · chain G against G, TM-score 1.00
- P19247 · AlphaFold monomer V2.0 prediction for cytolysin (P19247) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 P19247
- Elsewhere: RCSB PDB 4OWK · PDBe 4OWK · UniProt P19247
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