Research workbench
The active site of a carbohydrate esterase displays divergent catalytic and non-catalytic binding functions
Analyse The active site of a carbohydrate esterase displays divergent catalytic and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W9X
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acetyl xylan esterase
- UniProt
- B3PDE5
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative acetyl xylan esterase | protein | 312 | 30% helix, 24% strand | B3PDE5 |
| B | Putative acetyl xylan esterase | protein | 329 | 27% helix, 27% strand | B3PDE5 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.69 | 0.80 | 55 | empty |
| 2 | 197 | 0.58 | 0.81 | 27 | empty |
| 3 | 170 | 0.57 | 0.81 | 20 | empty |
| 4 | 50 | 0.51 | 0.88 | 14 | empty |
| 5 | 50 | 0.46 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 894 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2W9X · The active site of a carbohydrate esterase displays divergent catalytic and non-catalytic… · the same entry in another collection · chain A against A, TM-score 1.00
- B3PDE5 · AlphaFold monomer V2.0 prediction for acetylxylan esterase / glucomannan deacetylase… · a predicted model of the same protein · chain A 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 B3PDE5
- Elsewhere: RCSB PDB 2W9X · PDBe 2W9X · UniProt B3PDE5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.