Research workbench
The complex structure of xylc with xylose
Analyse The complex structure of xylc with xylose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VSV
- Type
- protein
- Length
- 2,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylosidase
- EC
- 3.2.1.37
- UniProt
- A2ICH1
- Ligands
- XYP, XYS
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylosidase (EC 3.2.1.37) | protein | 638 | 10% helix, 36% strand | A2ICH1 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 26 copies · chains A, C, B, D
- XYS · alpha-D-xylopyranose · sugar · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.89 | 0.92 | 112 | XYP |
| 2 | 488 | 0.86 | 0.92 | 59 | empty |
| 3 | 287 | 0.82 | 0.94 | 38 | empty |
| 4 | 302 | 0.82 | 0.93 | 47 | XYP |
| 5 | 325 | 0.67 | 0.81 | 37 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1938 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1923 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 803 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 789 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 787 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VSV · The complex structure of XylC with xylose · the same entry in another collection · 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 A2ICH1
- Elsewhere: RCSB PDB 3VSV · PDBe 3VSV · UniProt A2ICH1
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