MolNFT v1 · #20426 · protein
Endo-1,4-beta-xylanase II complex with 2,3-epoxypropyl-beta-D-xyloside
1REF: “Endo-1,4-beta-xylanase II complex with 2,3-epoxypropyl-beta-D-xyloside”. X-ray diffraction, 2 ligands (BEZ, C3X), 3 pockets (best druggability 0.55). MolNFT v1 #20426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1REF
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase II
- EC
- 3.2.1.8
- UniProt
- P36217
- Ligands
- BEZ, C3X
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase II (EC 3.2.1.8) | protein | 190 | 5% helix, 61% strand | P36217 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains B
- C3X · (2R)-oxiran-2-ylmethyl beta-D-xylopyranoside · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.55 | 0.78 | 36 | C3X |
| 2 | 238 | 0.47 | 0.73 | 35 | empty |
| 3 | 54 | 0.33 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 187 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (cyclization, covalent ligand).
Compared structures
- 1REF · Endo-1,4-beta-xylanase II complex with 2,3-epoxypropyl-beta-D-xyloside · the same entry in another collection · chain A against A, TM-score 1.00
- P36217 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase 2 (P36217) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P36217
- Elsewhere: RCSB PDB 1REF · PDBe 1REF · UniProt P36217
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