Research workbench
Structure analysis of a xylanase from glycosyl hydrolase family thirty: carbohydrate ligand complexes reveal this family of enzymes unique mechanism of substrate specificity and recognition
Analyse Structure analysis of a xylanase from glycosyl hydrolase family thirty… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KL5
- Type
- protein
- Length
- 1,535 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucuronoxylanase xync
- EC
- 3.2.1.136
- UniProt
- Q45070
- Ligands
- GCV, XYP
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 389 | 26% helix, 33% strand | Q45070 |
| B | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 390 | 27% helix, 34% strand | Q45070 |
| D | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 367 | 22% helix, 29% strand | Q45070 |
Ligands and binding sites
- GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · 4 copies · chains A, B, C, D
- XYP · beta-D-xylopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.80 | 0.82 | 97 | empty |
| 2 | 1141 | 0.72 | 0.76 | 99 | XYP, GCV |
| 3 | 942 | 0.71 | 0.75 | 74 | empty |
| 4 | 278 | 0.60 | 0.79 | 36 | empty |
| 5 | 252 | 0.57 | 0.78 | 32 | empty |
Interfaces
4 interfaces between chains.
- B–C · 881 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 585 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 466 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KL5 · Structure Analysis of a Xylanase From Glycosyl Hydrolase Family Thirty: Carbohydrate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q45070 · AlphaFold monomer V2.0 prediction for glucuronoxylanase xync (Q45070) · 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 Q45070
- Elsewhere: RCSB PDB 3KL5 · PDBe 3KL5 · UniProt Q45070
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