MolNFT v1 · #84354 · protein
Structure of fae solved by sad from data collected by direct data collection (ddc) using the grob robot goniometer
3ZI7 · Endo-1,4-beta-xylanase Y: “Structure of fae solved by sad from data collected by direct data collection (ddc) using the grob robot…”. X-ray diffraction, 1 ligand (CD), 8 pockets (best druggability 0.50). MolNFT v1 #84354 on…
- 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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