MolNFT v1 · #88652 · protein
The structure of the GH35 beta-galactosidase BGL35A from cellvibrio japonicus
4D1I · Beta-galactosidase, putative, BGL35A: “The structure of the GH35 beta-galactosidase BGL35A from cellvibrio japonicus”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.67). MolNFT v1 #88652 on GenesisL1: 3D…
- PDB
- 4D1I
- Type
- protein
- Length
- 4,313 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
- NA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 539 | 35% helix, 29% strand | B3PBE0 |
| G | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 540 | 34% helix, 29% strand | B3PBE0 |
Ligands and binding sites
- NA · Sodium ion · metal · 17 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · 3 copies · chains D, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.67 | 0.75 | 53 | empty |
| 2 | 500 | 0.65 | 0.77 | 63 | empty |
| 3 | 463 | 0.65 | 0.77 | 51 | empty |
| 4 | 496 | 0.65 | 0.77 | 65 | empty |
| 5 | 455 | 0.64 | 0.77 | 59 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1341 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1340 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1328 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1327 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 1326 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4D1I · The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicus · 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 4D1I · PDBe 4D1I · UniProt B3PBE0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.