Research workbench
Crystal structure of the catalytic domain of the modular laminarinase zglamc mutant E142S in complex with a thio-oligosaccharide
Analyse Crystal structure of the catalytic domain of the modular laminarinase zglamc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CTE
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,3-beta-glucanase, family GH16
- EC
- 3.2.1.39
- UniProt
- G0L2L9
- Ligands
- GS1, BGC, CA, NA, CL
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,3-beta-glucanase, family GH16 (EC 3.2.1.39) | protein | 231 | 11% helix, 53% strand | G0L2L9 |
Ligands and binding sites
- GS1 · 1-thio-beta-D-glucopyranose · ligand · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.57 | 0.79 | 32 | GS1, CL, EDO, GOL |
| 2 | 189 | 0.53 | 0.78 | 29 | GS1, EDO, GOL |
Interfaces
1 interface between chains.
- A–B · 403 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4CTE · Crystal structure of the catalytic domain of the modular laminarinase ZgLamC mutant E142S… · 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
- Every structure of UniProt G0L2L9
- Elsewhere: RCSB PDB 4CTE · PDBe 4CTE · UniProt G0L2L9
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