Research workbench
Crystal structure of human beta-galactosidase in complex with nbt-dgj
Analyse Crystal structure of human beta-galactosidase in complex with nbt-dgj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WF2
- 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
- NDJ, NAG, SO4, CL
- Pockets
- 20 · best druggability 0.82
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, 30% strand | P16278 |
Ligands and binding sites
- NDJ · (2R,3S,4R,5S)-N-butyl-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide · 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 | 1101 | 0.82 | 0.83 | 116 | NAG, EDO |
| 2 | 1118 | 0.81 | 0.83 | 106 | NAG, EDO |
| 3 | 709 | 0.70 | 0.77 | 60 | EDO |
| 4 | 702 | 0.70 | 0.77 | 58 | empty |
| 5 | 535 | 0.68 | 0.78 | 46 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 901 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 838 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 380 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
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 3WF2 · PDBe 3WF2 · UniProt P16278
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