Research workbench
Crystal structure of human beta-galactosidase in complex with 6S-nbi- dgj
Analyse Crystal structure of human beta-galactosidase in complex with 6S-nbi- dgj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WF0
- Type
- protein
- Length
- 2,416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P16278
- Ligands
- 6DJ, NAG, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23) | protein | 605 | 24% helix, 29% strand | P16278 |
| C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 603 | 24% helix, 29% strand | P16278 |
Ligands and binding sites
- 6DJ · (3Z,6S,7R,8S,8aS)-3-(butylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-6,7,8-triol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.81 | 0.82 | 102 | NAG, EDO |
| 2 | 1035 | 0.81 | 0.82 | 97 | NAG, EDO |
| 3 | 532 | 0.70 | 0.79 | 54 | empty |
| 4 | 536 | 0.68 | 0.78 | 47 | EDO |
| 5 | 460 | 0.68 | 0.79 | 46 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 923 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 921 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 844 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WF0 · Crystal structure of human beta-galactosidase in complex with 6S-NBI-DGJ · the same entry in another collection · chain D against D, TM-score 1.00
- P16278 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P16278) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P16278
- Elsewhere: RCSB PDB 3WF0 · PDBe 3WF0 · UniProt P16278
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