Research workbench
Structure of a new family of polysaccharide lyase PL25-ulvanlyase.
Analyse Structure of a new family of polysaccharide lyase PL25-ulvanlyase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UAM
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ulvan lyase-PL25
- Ligands
- ZN, K, CL, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ulvan lyase-PL25 | protein | 440 | 6% helix, 46% strand | — |
| B | Ulvan lyase-PL25 | protein | 440 | 6% helix, 46% strand | — |
Ligands and binding sites
- 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
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 394 | 0.72 | 0.84 | 54 | GOL, EDO |
| 2 | 503 | 0.68 | 0.79 | 56 | CL, PO4, K, EDO |
| 3 | 435 | 0.67 | 0.80 | 44 | CL, PO4, K, EDO |
| 4 | 295 | 0.62 | 0.79 | 32 | empty |
| 5 | 286 | 0.61 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 446 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5UAM · Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase. · 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 5UAM · PDBe 5UAM
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