MolNFT v1 · #5026 · protein
E246C mutant of P fluorescens subsp. cellulosa xylanase a in complex with xylopentaose
1E5N · Endo-1,4-beta-xylanase a: “E246C mutant of P fluorescens subsp. cellulosa xylanase a in complex with xylopentaose”. X-ray diffraction, 2 ligands (XYP, CA), 4 pockets (best druggability 0.81). MolNFT v1 #5026 on GenesisL1: 3D…
- PDB
- 1E5N
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase a
- EC
- 3.2.1.8
- UniProt
- P14768
- Ligands
- XYP, CA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 346 | 37% helix, 20% strand | P14768 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 10 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.81 | 0.82 | 101 | XYP |
| 2 | 142 | 0.49 | 0.79 | 29 | empty |
| 3 | 154 | 0.48 | 0.77 | 31 | empty |
| 4 | 50 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1011 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1E5N · E246C mutant of P fluorescens subsp. cellulosa xylanase A in complex with xylopentaose · the same entry in another collection · chain A against A, TM-score 1.00
- P14768 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P14768) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P14768
- Elsewhere: RCSB PDB 1E5N · PDBe 1E5N · UniProt P14768
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