Research workbench
Structure of a beta galactosidase with inhibitor
Analyse Structure of a beta galactosidase with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JAW
- Type
- protein
- Length
- 4,249 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
- UUU, NA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 537 | 34% helix, 29% strand | B3PBE0 |
| B | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 528 | 34% helix, 29% strand | B3PBE0 |
| C | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 536 | 34% helix, 29% strand | B3PBE0 |
| D | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 532 | 32% helix, 30% strand | B3PBE0 |
| E | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 533 | 33% helix, 29% strand | B3PBE0 |
| F | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 525 | 32% helix, 30% strand | B3PBE0 |
| G | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 531 | 34% helix, 30% strand | B3PBE0 |
| H | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 527 | 33% helix, 30% strand | B3PBE0 |
Ligands and binding sites
- UUU · (1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol · ligand · 8 copies · chains A, D, B, C, E, F, G, H
- NA · Sodium ion · metal · 25 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · chains E
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 | 784 | 0.69 | 0.76 | 81 | UUU |
| 2 | 650 | 0.68 | 0.76 | 60 | UUU |
| 3 | 517 | 0.65 | 0.77 | 59 | empty |
| 4 | 451 | 0.65 | 0.77 | 59 | UUU |
| 5 | 414 | 0.64 | 0.78 | 57 | UUU |
Interfaces
13 interfaces between chains.
- G–H · 1350 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 1325 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1317 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1308 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 345 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5JAW · Structure of a beta galactosidase with inhibitor · 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 5JAW · PDBe 5JAW · UniProt B3PBE0
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