Research workbench
Structure of fae solved by sad from data collected by direct data collection (ddc) using the grob robot goniometer
Analyse Structure of fae solved by sad from data collected by direct data collection… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZI7
- 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 0.50
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 · 12 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.50 | 0.82 | 26 | empty |
| 2 | 92 | 0.44 | 0.80 | 21 | empty |
| 3 | 90 | 0.39 | 0.77 | 22 | empty |
| 4 | 68 | 0.38 | 0.79 | 20 | empty |
| 5 | 82 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, phosphorylation).
Compared structures
- 3ZI7 · Structure of fae solved by sad from data collected by direct data collection (ddc) using… · 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 3ZI7 · PDBe 3ZI7 · UniProt P51584
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