Research workbench
Feruloyl esterase domain of xyny from clostridium thermocellum before exposure to 266NM UV laser
Analyse Feruloyl esterase domain of xyny from clostridium thermocellum before exposure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H35
- 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
- CD
- Pockets
- 8 · best druggability 0.55
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
- CD · Cadmium ion · metal · 8 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.55 | 0.81 | 27 | empty |
| 2 | 165 | 0.55 | 0.81 | 27 | empty |
| 3 | 52 | 0.41 | 0.82 | 18 | empty |
| 4 | 56 | 0.38 | 0.80 | 17 | empty |
| 5 | 83 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, phosphorylation).
Compared structures
- 4H35 · Feruloyl Esterase Domain of XYNY from Clostridium thermocellum before exposure to 266nm… · 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 4H35 · PDBe 4H35 · UniProt P51584
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