Research workbench
Crystal structure of S. pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin C
Analyse Crystal structure of S. pneumoniae hyaluronate lyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W3Y
- Type
- protein
- Length
- 721 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronate lyase
- EC
- 4.2.2.1
- UniProt
- Q54873
- Ligands
- XYL, PVC, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronate lyase (EC 4.2.2.1) | protein | 721 | 35% helix, 26% strand | Q54873 |
Ligands and binding sites
- XYL · Xylitol · ligand · 2 copies · chains A
- PVC · (2E,4R,5S)-2,3,4,5-tetrahydroxy-6-(palmitoyloxy)hex-2-enoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.73 | 0.78 | 63 | PVC |
| 2 | 116 | 0.49 | 0.80 | 28 | empty |
| 3 | 169 | 0.43 | 0.74 | 31 | SO4 |
| 4 | 98 | 0.42 | 0.78 | 26 | empty |
| 5 | 89 | 0.40 | 0.77 | 17 | empty |
Compared structures
- 1W3Y · Crystal structure of S. pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin C · the same entry in another collection · chain A against A, TM-score 1.00
- Q54873 · AlphaFold monomer V2.0 prediction for hyaluronate lyase (Q54873) · 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 Q54873
- Elsewhere: RCSB PDB 1W3Y · PDBe 1W3Y · UniProt Q54873
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