Research workbench
S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with vanillate
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
- 1WB6
- 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
- VXX, CD
- Pockets
- 7 · best druggability 0.44
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
- VXX · Methyl vanillate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 20 copies · chains A, B
- GOL · Glycerol · additive · 7 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
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.44 | 0.82 | 18 | GOL |
| 2 | 63 | 0.38 | 0.79 | 16 | empty |
| 3 | 86 | 0.38 | 0.77 | 17 | empty |
| 4 | 50 | 0.37 | 0.81 | 19 | GOL |
| 5 | 88 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1WB6 · 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 1WB6 · PDBe 1WB6 · UniProt P51584
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