Research workbench
S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with syringate
Analyse S954A mutant of the feruloyl esterase module from clostridium thermocellum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WB5
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase Y
- EC
- 3.2.1.8
- UniProt
- P51584
- Ligands
- SYR, CD
- Pockets
- 8 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase Y (EC 3.2.1.8) | protein | 283 | 33% helix, 20% strand | P51584 |
Ligands and binding sites
- SYR · Syringate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 17 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.45 | 0.82 | 19 | empty |
| 2 | 77 | 0.40 | 0.78 | 17 | empty |
| 3 | 89 | 0.38 | 0.76 | 12 | empty |
| 4 | 79 | 0.37 | 0.77 | 17 | empty |
| 5 | 54 | 0.37 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1048 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1WB5 · S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P51584 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase Y (P51584) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P51584
- Elsewhere: RCSB PDB 1WB5 · PDBe 1WB5 · UniProt P51584
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.