MolNFT v1 · #62688 · protein
Crystal structure of xylanase xynb from paenibacillus barcinonensis complexed with a conduramine derivative
3EMZ · Endo-1,4-beta-xylanase: “Crystal structure of xylanase xynb from paenibacillus barcinonensis complexed with a conduramine derivative”. X-ray diffraction, 1 ligand (HXH), 2 pockets (best druggability 0.57). MolNFT v1 #62688 on…
- PDB
- 3EMZ
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- O69231
- Ligands
- HXH
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 331 | 39% helix, 18% strand | O69231 |
Ligands and binding sites
- HXH · (1S,2S,3R,6R)-6-[(4-phenoxybenzyl)amino]cyclohex-4-ene-1,2,3-triol · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.57 | 0.77 | 36 | HXH |
| 2 | 50 | 0.28 | 0.75 | 13 | empty |
Compared structures
- 3EMZ · Crystal structure of xylanase XynB from Paenibacillus barci nsis complexed with a… · the same entry in another collection · chain A against A, TM-score 1.00
- O69231 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase B (O69231) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O69231
- Elsewhere: RCSB PDB 3EMZ · PDBe 3EMZ · UniProt O69231
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