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
- 6TBJ
- Type
- protein
- Length
- 4,223 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
- N0W, NA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 8 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 525 | 33% helix, 30% strand | B3PBE0 |
| B | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 524 | 33% helix, 30% strand | B3PBE0 |
| C | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 525 | 33% helix, 30% strand | B3PBE0 |
| D | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 531 | 33% helix, 30% strand | B3PBE0 |
| E | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 532 | 33% helix, 29% strand | B3PBE0 |
| F | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 531 | 33% helix, 29% strand | B3PBE0 |
| G | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 532 | 33% helix, 30% strand | B3PBE0 |
| H | Beta-galactosidase, putative, BGL35A (EC 3.2.1.23) | protein | 523 | 33% helix, 30% strand | B3PBE0 |
Ligands and binding sites
- N0W · 5-(dimethylamino)-~{N}-[6-[(2~{S},3~{R},4~{S},5~{R})-3-(hydroxymethyl)-4,5-bis(oxidanyl)piperidin-2-yl]hexyl]naphthalene-1-sulfonamide · ligand · 8 copies · chains A, C, B, H, D, E, G, F
- NA · Sodium ion · metal · 27 copies · chains A, B, C, D, E, F, G, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.67 | 0.78 | 52 | N0W |
| 2 | 499 | 0.67 | 0.78 | 58 | N0W |
| 3 | 507 | 0.65 | 0.77 | 57 | N0W |
| 4 | 474 | 0.65 | 0.77 | 52 | N0W |
| 5 | 490 | 0.64 | 0.76 | 58 | N0W |
Interfaces
9 interfaces between chains.
- D–F · 1353 Ų buried · 24 hydrogen bonds · protein-protein
- C–H · 1342 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1340 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1338 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1335 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6TBJ · 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 6TBJ · PDBe 6TBJ · UniProt B3PBE0
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