Research workbench
Beta-D-xylosidase (selenomethionine) xynd from clostridium acetobutylicum
Analyse Beta-D-xylosidase (selenomethionine) xynd from clostridium acetobutylicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YI7
- Type
- protein
- Length
- 2,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase, family 43 glycosyl hydrolase
- EC
- 3.2.1.37
- UniProt
- Q97DM1
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-xylosidase, family 43 glycosyl hydrolase (EC 3.2.1.37) | protein | 534 | 1% helix, 47% strand | Q97DM1 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 20 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.79 | 0.83 | 45 | empty |
| 2 | 697 | 0.79 | 0.83 | 42 | empty |
| 3 | 789 | 0.72 | 0.77 | 94 | GOL |
| 4 | 316 | 0.68 | 0.82 | 28 | empty |
| 5 | 313 | 0.66 | 0.81 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2104 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2075 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 954 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 952 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1YI7 · Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum · 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 Q97DM1
- Elsewhere: RCSB PDB 1YI7 · PDBe 1YI7 · UniProt Q97DM1
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