Research workbench
Structure of fae solved by sad from data collected at the peak of the selenium absorption edge on ID30B
Analyse Structure of fae solved by sad from data collected at the peak of the selenium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FJ4
- Type
- protein
- Length
- 283 residues
- Chains
- 1
- 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, SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase Y (EC 3.2.1.8) | protein | 283 | 33% helix, 19% strand | P51584 |
Ligands and binding sites
- CD · Cadmium ion · metal · 5 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.46 | 0.83 | 22 | empty |
| 2 | 73 | 0.35 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 9 modified (engineered, phosphorylation).
Compared structures
- 6FJ4 · Structure of FAE solved by SAD from data collected at the peak of the Selenium absorption… · 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 6FJ4 · PDBe 6FJ4 · UniProt P51584
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