Research workbench
Crystal structure of the yeast gal regulon complex of the repressor, GAL80P, and the transducer, GAL3P, with galactose and ATP
Analyse Crystal structure of the yeast gal regulon complex of the repressor, GAL80P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V2U
- Type
- protein
- Length
- 1,841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GALACTOSE/LACTOSE metabolism regulatory protein GAL80; Protein GAL3
- UniProt
- P04387, P13045
- Ligands
- ATP, GLA, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GALACTOSE/LACTOSE metabolism regulatory protein GAL80 | protein | 409 | 33% helix, 27% strand | P04387 |
| B | GALACTOSE/LACTOSE metabolism regulatory protein GAL80 | protein | 402 | 33% helix, 28% strand | P04387 |
| C | Protein GAL3 | protein | 516 | 45% helix, 18% strand | P13045 |
| D | Protein GAL3 | protein | 514 | 45% helix, 19% strand | P13045 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, D, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.82 | 0.89 | 36 | empty |
| 2 | 680 | 0.81 | 0.85 | 68 | GOL |
| 3 | 863 | 0.77 | 0.80 | 119 | empty |
| 4 | 438 | 0.75 | 0.84 | 71 | MG, GLA, ATP |
| 5 | 875 | 0.74 | 0.78 | 94 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1905 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1492 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1334 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3V2U · Crystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the… · the same entry in another collection · chain D against D, TM-score 1.00
- P04387 · AlphaFold monomer V2.0 prediction for GALACTOSE/LACTOSE metabolism regulatory protein… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P13045 · AlphaFold monomer V2.0 prediction for protein GAL3 (P13045) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P04387
- Every structure of UniProt P13045
- Elsewhere: RCSB PDB 3V2U · PDBe 3V2U · UniProt P04387 · UniProt P13045
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