Research workbench
Crystal structure of streptococcus agalactiae hyaluronate lyase complexed with hexasaccharide unit of hyaluronan
Analyse Crystal structure of streptococcus agalactiae hyaluronate lyase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LXM
- Type
- protein
- Length
- 794 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronate lyase
- EC
- 4.2.2.1
- UniProt
- Q53591
- Ligands
- NAG, BDP
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronate lyase (EC 4.2.2.1) | protein | 794 | 32% helix, 28% strand | Q53591 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.68 | 0.77 | 78 | BDP, NAG |
| 2 | 292 | 0.63 | 0.80 | 29 | empty |
| 3 | 262 | 0.54 | 0.76 | 31 | empty |
| 4 | 170 | 0.47 | 0.76 | 24 | empty |
| 5 | 100 | 0.39 | 0.76 | 21 | empty |
Compared structures
- 1LXM · Crystal Structure of Streptococcus agalactiae Hyaluronate Lyase Complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q53591 · AlphaFold monomer V2.0 prediction for hyaluronate lyase (Q53591) · 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 Q53591
- Elsewhere: RCSB PDB 1LXM · PDBe 1LXM · UniProt Q53591
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