MolNFT v1 · #62666 · protein
Crystal structure of xynb, an intracellular xylanase from paenibacillus barcinonensis
3EMC · Endo-1,4-beta-xylanase: “Crystal structure of xynb, an intracellular xylanase from paenibacillus barcinonensis”. X-ray diffraction, 2 pockets (best druggability 0.59). MolNFT v1 #62666 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3EMC
- 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
- Pockets
- 2 · best druggability 0.59
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
- MPD · (4S)-2-methyl-2,4-pentanediol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.59 | 0.77 | 37 | MPD |
| 2 | 51 | 0.29 | 0.75 | 13 | empty |
Compared structures
- 3EMC · Crystal structure of XynB, an intracellular xylanase from Paenibacillus barci nsis · 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 3EMC · PDBe 3EMC · UniProt O69231
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