Research workbench
The structure of the GH35 beta-galactosidase BGL35A from cellvibrio japonicas in complex with 1-deoxygalactonojirimycin
Analyse The structure of the GH35 beta-galactosidase BGL35A from cellvibrio japonicas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D1J
- Type
- protein
- Length
- 4,314 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase, putative, BGL35A
- EC
- 3.2.1.23
- UniProt
- B3PBE0
- Ligands
- DGJ, NA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, H | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 539 | 35% helix, 29% strand | B3PBE0 |
| D, G | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 540 | 35% helix, 29% strand | B3PBE0 |
Ligands and binding sites
- DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 8 copies · chains A, C, B, H, D, E, G, F
- NA · Sodium ion · metal · 23 copies · chains A, B, D, E, F, G, H
- ACT · Acetate ion · additive · 5 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.68 | 0.78 | 59 | DGJ |
| 2 | 536 | 0.66 | 0.77 | 61 | DGJ |
| 3 | 506 | 0.66 | 0.77 | 54 | DGJ |
| 4 | 523 | 0.65 | 0.77 | 49 | DGJ |
| 5 | 460 | 0.65 | 0.77 | 59 | DGJ |
Interfaces
9 interfaces between chains.
- C–H · 1340 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1334 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1330 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1330 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1330 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4D1J · The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicas in complex… · 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 B3PBE0
- Elsewhere: RCSB PDB 4D1J · PDBe 4D1J · UniProt B3PBE0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.