MolNFT v1 · #135831 · protein
Structure of a new family of polysaccharide lyase PL25-ulvanlyase bound to -[GLCA(1-4)RHA3S]-
5UAS · Ulvanlyase-PL25: “Structure of a new family of polysaccharide lyase PL25-ulvanlyase bound to -[GLCA(1-4)RHA3S]-”. X-ray diffraction, 6 ligands (83Y, GCD, BDP), 7 pockets (best druggability 0.74). MolNFT v1 #135831 on GenesisL1: 3D…
- PDB
- 5UAS
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ulvanlyase-PL25
- Ligands
- 83Y, GCD, BDP, ZN, K, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ulvanlyase-PL25 | protein | 440 | 6% helix, 48% strand | — |
| B | Ulvanlyase-PL25 | protein | 440 | 6% helix, 48% strand | — |
Ligands and binding sites
- 83Y · 3-O-sulfo-alpha-L-rhamnopyranose · ligand · 4 copies · chains A, B
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.74 | 0.85 | 44 | empty |
| 2 | 511 | 0.68 | 0.78 | 48 | 83Y, BDP, GCD, K, CL, EDO |
| 3 | 506 | 0.68 | 0.79 | 52 | 83Y, BDP, GCD, K, CL, EDO |
| 4 | 294 | 0.63 | 0.80 | 29 | empty |
| 5 | 305 | 0.62 | 0.79 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5UAS · Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase bound to… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5UAS · PDBe 5UAS
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