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Crystal structure of a cold-adapted dimeric beta-D-galactosidase from paracoccus sp. 32D strain
Analyse Crystal structure of a cold-adapted dimeric beta-D-galactosidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EUV
- Type
- protein
- Length
- 1,462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-galactosidase
- UniProt
- D1LZK0
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-D-galactosidase | protein | 731 | 15% helix, 36% strand | D1LZK0 |
Ligands and binding sites
- ACT · Acetate ion · additive · 8 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.78 | 0.90 | 53 | empty |
| 2 | 926 | 0.77 | 0.79 | 90 | empty |
| 3 | 610 | 0.71 | 0.79 | 49 | empty |
| 4 | 581 | 0.71 | 0.79 | 47 | empty |
| 5 | 257 | 0.64 | 0.81 | 34 | ACT |
Interfaces
1 interface between chains.
- A–B · 2558 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5EUV · Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d… · the same entry in another collection · chain B against B, 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 D1LZK0
- Elsewhere: RCSB PDB 5EUV · PDBe 5EUV · UniProt D1LZK0
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