MolNFT v1 · #125602 · protein
Crystal structure of a cold-adapted dimeric beta-D-galactosidase from paracoccus sp. 32D strain in complex with galactose
5LDR: “Crystal structure of a cold-adapted dimeric beta-D-galactosidase from paracoccus sp. 32D strain in complex…”. X-ray diffraction, 3 ligands (GAL, GLC, CL), 12 pockets (best druggability 0.80). MolNFT v1 #125602 on GenesisL1: 3D…
- PDB
- 5LDR
- Type
- protein
- Length
- 1,462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-galactosidase
- EC
- 3.2.1.23
- UniProt
- D1LZK0
- Ligands
- GAL, GLC, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-D-galactosidase (EC 3.2.1.23) | protein | 731 | 13% helix, 34% strand | D1LZK0 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.80 | 0.81 | 118 | GAL |
| 2 | 258 | 0.77 | 0.90 | 43 | empty |
| 3 | 184 | 0.71 | 0.88 | 31 | empty |
| 4 | 606 | 0.71 | 0.79 | 43 | PEG |
| 5 | 568 | 0.69 | 0.79 | 41 | ACT |
Interfaces
1 interface between chains.
- A–B · 2625 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5LDR · Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d… · 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 D1LZK0
- Elsewhere: RCSB PDB 5LDR · PDBe 5LDR · UniProt D1LZK0
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