MolNFT v1 · #17139 · protein
Specificity and mechanism of streptococcus pneumoniae hyaluronate lyase: complex with 6-sulphated chondroitin disaccharide
1OJP: “Specificity and mechanism of streptococcus pneumoniae hyaluronate lyase: complex with 6-sulphated chondroitin…”. X-ray diffraction, 3 ligands (NG6, GCD, SO4), 8 pockets (best druggability 0.74). MolNFT v1 #17139 on GenesisL1: 3D…
- PDB
- 1OJP
- Type
- protein
- Length
- 722 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
- NG6, GCD, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronate lyase (EC 4.2.2.1) | protein | 722 | 36% helix, 27% strand | Q54873 |
Ligands and binding sites
- NG6 · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose · ligand · chains A
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.74 | 0.78 | 63 | NG6, GCD |
| 2 | 83 | 0.44 | 0.80 | 20 | empty |
| 3 | 101 | 0.40 | 0.77 | 25 | empty |
| 4 | 95 | 0.40 | 0.77 | 18 | empty |
| 5 | 94 | 0.39 | 0.77 | 19 | empty |
Compared structures
- 1OJP · Specificity and mechanism of streptococcus pneumoniae hyaluronate lyase: complex with… · 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 1OJP · PDBe 1OJP · UniProt Q54873
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