Research workbench
The crystal structure of rice (oryza sativa L.) OS4BGLU12 with dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
Analyse The crystal structure of rice (oryza sativa L.) OS4BGLU12 with dinitrophenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PTQ
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase OS4BGLU12
- EC
- 3.2.1.21
- UniProt
- Q01KB2
- Ligands
- NFG, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase OS4BGLU12 (EC 3.2.1.21) | protein | 478 | 44% helix, 17% strand | Q01KB2 |
Ligands and binding sites
- NFG · 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.73 | 0.77 | 125 | GOL |
| 2 | 428 | 0.71 | 0.82 | 43 | NFG |
| 3 | 442 | 0.71 | 0.81 | 43 | NFG |
| 4 | 91 | 0.44 | 0.80 | 21 | empty |
| 5 | 61 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 455 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3PTQ · The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with dinitrophenyl… · 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 Q01KB2
- Elsewhere: RCSB PDB 3PTQ · PDBe 3PTQ · UniProt Q01KB2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.