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Crystal structure of the catalytic mutant XYN52B2-E335G, a GH52 beta- D-xylosidase from geobacillus stearothermophilus T6
Analyse Crystal structure of the catalytic mutant XYN52B2-E335G, a GH52 beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RHH
- Type
- protein
- Length
- 2,777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- UniProt
- Q09LZ0
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylosidase | protein | 694 | 37% helix, 22% strand | Q09LZ0 |
| C | Beta-xylosidase | protein | 696 | 36% helix, 22% strand | Q09LZ0 |
| D | Beta-xylosidase | protein | 693 | 37% helix, 22% strand | Q09LZ0 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 7 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.79 | 0.90 | 40 | empty |
| 2 | 319 | 0.78 | 0.89 | 34 | empty |
| 3 | 1048 | 0.77 | 0.79 | 140 | TRS |
| 4 | 508 | 0.73 | 0.82 | 81 | TRS |
| 5 | 430 | 0.72 | 0.83 | 67 | TRS |
Interfaces
3 interfaces between chains.
- A–B · 2486 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2408 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RHH · Crystal structure of the catalytic mutant Xyn52B2-E335G, a GH52 Beta-D-xylosidase from… · 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 Q09LZ0
- Elsewhere: RCSB PDB 4RHH · PDBe 4RHH · UniProt Q09LZ0
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