MolNFT v1 · #2810 · protein
Mechanism of hyaluronan binding and degradation: structure of streptococcus pneumoniae hyaluronate lyase in complex with hyaluronic acid disaccharide at 1.7 a resolution
1C82: “Mechanism of hyaluronan binding and degradation: structure of streptococcus pneumoniae hyaluronate lyase in…”. X-ray diffraction, 3 ligands (GCD, NAG, NA), 6 pockets (best druggability 0.74). MolNFT v1 #2810 on GenesisL1: 3D…
- PDB
- 1C82
- Type
- protein
- Length
- 719 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
- GCD, NAG, NA
- Pockets
- 6 · 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 | 719 | 35% helix, 26% strand | Q54873 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CAC · Cacodylate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.74 | 0.78 | 68 | NAG, GCD |
| 2 | 86 | 0.42 | 0.79 | 19 | empty |
| 3 | 127 | 0.38 | 0.73 | 31 | empty |
| 4 | 55 | 0.36 | 0.79 | 13 | empty |
| 5 | 69 | 0.36 | 0.78 | 15 | empty |
Compared structures
- 1C82 · Mechanism of hyaluronan binding and degradation: structure of streptococcus pneumoniae… · 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 1C82 · PDBe 1C82 · UniProt Q54873
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