MolNFT v1 · #102379 · protein
Crystal structure of ALG17C mutant Y258A complexed with alginate trisaccharide
4OJZ · Putative alginate lyase: “Crystal structure of ALG17C mutant Y258A complexed with alginate trisaccharide”. X-ray diffraction, 4 ligands (LGU, MAV, BEM), 12 pockets (best druggability 0.81). MolNFT v1 #102379 on GenesisL1: 3D…
- PDB
- 4OJZ
- Type
- protein
- Length
- 1,411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alginate lyase
- UniProt
- Q21FJ0
- Ligands
- LGU, MAV, BEM, ZN
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alginate lyase | protein | 706 | 36% helix, 28% strand | Q21FJ0 |
| B | Putative alginate lyase | protein | 705 | 36% helix, 29% strand | Q21FJ0 |
Ligands and binding sites
- LGU · alpha-L-gulopyranuronic acid · ligand · 2 copies · chains A, B
- MAV · alpha-D-mannopyranuronic acid · ligand · 2 copies · chains A, B
- BEM · beta-D-mannopyranuronic acid · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.81 | 0.84 | 88 | LGU, MAV, BEM |
| 2 | 762 | 0.81 | 0.84 | 90 | LGU, MAV, BEM |
| 3 | 1123 | 0.74 | 0.77 | 87 | empty |
| 4 | 66 | 0.43 | 0.81 | 20 | empty |
| 5 | 103 | 0.42 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2703 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 4OJZ · Crystal Structure of Alg17c Mutant Y258A Complexed with Alginate Trisaccharide · the same entry in another collection · chain A against A, TM-score 1.00
- Q21FJ0 · AlphaFold monomer V2.0 prediction for exo-oligoalginate lyase (Q21FJ0) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q21FJ0
- Elsewhere: RCSB PDB 4OJZ · PDBe 4OJZ · UniProt Q21FJ0
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