Research workbench
E. COLI (lacz) beta-galactosidase (N460T) in complex with galactonolactone
Analyse E. COLI (lacz) beta-galactosidase (N460T) in complex with galactonolactone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VDB
- Type
- protein
- Length
- 4,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- P00722
- Ligands
- 149, NA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-galactosidase (EC 3.2.1.23) | protein | 1015 | 14% helix, 40% strand | P00722 |
Ligands and binding sites
- 149 · D-galactonolactone · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 14 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 77 copies · chains A, D, B, C
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 | 989 | 0.82 | 0.83 | 112 | empty |
| 2 | 789 | 0.81 | 0.84 | 112 | DMS |
| 3 | 719 | 0.78 | 0.83 | 74 | empty |
| 4 | 430 | 0.76 | 0.85 | 67 | DMS |
| 5 | 403 | 0.74 | 0.85 | 58 | DMS |
Interfaces
6 interfaces between chains.
- A–D · 2352 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2327 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2104 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2007 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3VDB · E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone · the same entry in another collection · chain D against D, TM-score 1.00
- P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain D 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 P00722
- Elsewhere: RCSB PDB 3VDB · PDBe 3VDB · UniProt P00722
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