MolNFT v1 · #102794 · protein
Crystal structure of the vibrio vulnificus HEMOLYSIN/CYTOLYSIN beta- trefoil lectin with N-acetyl-D-lactosamine bound
4OWL: “Crystal structure of the vibrio vulnificus HEMOLYSIN/CYTOLYSIN beta- trefoil lectin with…”. X-ray diffraction, 2 ligands (GAL, NAG), 7 pockets (best druggability 0.33). MolNFT v1 #102794 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4OWL
- Type
- protein
- Length
- 925 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytolysin
- UniProt
- P19247
- Ligands
- GAL, NAG
- Pockets
- 7 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytolysin | protein | 132 | 7% helix, 43% strand | P19247 |
| B, C, F, G | Cytolysin | protein | 131 | 7% helix, 45% strand | P19247 |
| D | Cytolysin | protein | 137 | 7% helix, 45% strand | P19247 |
| E | Cytolysin | protein | 132 | 7% helix, 45% strand | P19247 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains B, C, D, E, F, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.33 | 0.76 | 14 | empty |
| 2 | 60 | 0.33 | 0.77 | 15 | empty |
| 3 | 54 | 0.33 | 0.78 | 20 | empty |
| 4 | 50 | 0.30 | 0.77 | 15 | empty |
| 5 | 54 | 0.29 | 0.75 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–G · 445 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 442 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 439 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 427 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 405 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4OWL · 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 E 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 4OWL · PDBe 4OWL · UniProt P19247
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