Research workbench
Crystal structure analysis of the cold-adamped beta-galactosidase from rahnella sp. R3
Analyse Crystal structure analysis of the cold-adamped beta-galactosidase from rahnella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E9A
- Type
- protein
- Length
- 4,099 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- A0A0B4U8I5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 679 | 33% helix, 22% strand | A0A0B4U8I5 |
| B, C, D, E, F | Beta-galactosidase (EC 3.2.1.23) | protein | 684 | 32% helix, 22% strand | A0A0B4U8I5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.83 | 0.85 | 96 | empty |
| 2 | 80 | 0.76 | 0.99 | 28 | empty |
| 3 | 80 | 0.76 | 0.98 | 28 | empty |
| 4 | 84 | 0.76 | 0.98 | 29 | empty |
| 5 | 77 | 0.75 | 0.98 | 25 | empty |
Interfaces
11 interfaces between chains.
- B–C · 2319 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2313 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 2303 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2302 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2295 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5E9A · Crystal structure analysis of the cold-adamped beta-galactosidase from Rahnella sp. R3 · 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 A0A0B4U8I5
- Elsewhere: RCSB PDB 5E9A · PDBe 5E9A · UniProt A0A0B4U8I5
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