MolNFT v1 · #81785 · protein
Crystal structure of the yeast gal regulon complex of the repressor, GAL80P, and the transducer, GAL3P, with galactose and ATP
3V2U · GALACTOSE/LACTOSE metabolism regulatory protein GAL80: “Crystal structure of the yeast gal regulon complex of the repressor, GAL80P, and the transducer, GAL3P, with…”. X-ray diffraction, 3 ligands (ATP, GLA, MG), 20 pockets (best…
- 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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