MolNFT v1 · #32500 · protein
Native crystal structure of a GH39 beta-xylosidase XYNB1 from geobacillus stearothermophilus
2BS9: “Native crystal structure of a GH39 beta-xylosidase XYNB1 from geobacillus stearothermophilus”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.78). MolNFT v1 #32500 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2BS9
- Type
- protein
- Length
- 4,008 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- Q9ZFM2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Beta-xylosidase (EC 3.2.1.37) | protein | 501 | 32% helix, 26% strand | Q9ZFM2 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, C, D, E, F, G, H
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 | 934 | 0.78 | 0.80 | 97 | empty |
| 2 | 609 | 0.77 | 0.83 | 46 | empty |
| 3 | 874 | 0.76 | 0.79 | 97 | empty |
| 4 | 665 | 0.76 | 0.81 | 44 | empty |
| 5 | 552 | 0.75 | 0.82 | 46 | empty |
Interfaces
15 interfaces between chains.
- F–H · 2786 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 2782 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 2781 Ų buried · 59 hydrogen bonds · protein-protein
- E–G · 2769 Ų buried · 62 hydrogen bonds · protein-protein
- F–G · 1644 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2BS9 · Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9ZFM2 · AlphaFold monomer V2.0 prediction for beta-xylosidase (Q9ZFM2) · 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 Q9ZFM2
- Elsewhere: RCSB PDB 2BS9 · PDBe 2BS9 · UniProt Q9ZFM2
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