Research workbench
Crystal structure of S. pneumoniae hyaluronate lyase in complex with W249B
Analyse Crystal structure of S. pneumoniae hyaluronate lyase in complex with W249B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BRP
- 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
- XLS, SIE, SO4
- Pockets
- 10 · best druggability 0.74
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
- XLS · D-xylose · ligand · 3 copies · chains A
- SIE · Sulfamic acid 1-decyl-2-(4-sulfamoyloxyphenyl)-1H-indol-6-yl ester · 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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.74 | 0.78 | 69 | SIE |
| 2 | 51 | 0.70 | 0.98 | 25 | empty |
| 3 | 75 | 0.40 | 0.79 | 18 | empty |
| 4 | 87 | 0.40 | 0.78 | 18 | empty |
| 5 | 73 | 0.39 | 0.79 | 20 | empty |
Compared structures
- 2BRP · Crystal structure of S. pneumoniae hyaluronate lyase in complex with W249b · 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 2BRP · PDBe 2BRP · UniProt Q54873
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