Research workbench
Structure of nucleotidyltransferase complexed with udp-galactose
Analyse Structure of nucleotidyltransferase complexed with udp-galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GUP
- Type
- protein
- Length
- 1,379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-1-phosphate uridylyltransferase
- EC
- 2.7.7.10
- UniProt
- P09148
- Ligands
- GDU, ZN, FE, K
- Pockets
- 10 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactose-1-phosphate uridylyltransferase (EC 2.7.7.10) | protein | 347 | 29% helix, 20% strand | P09148 |
| B, C, D | Galactose-1-phosphate uridylyltransferase (EC 2.7.7.10) | protein | 344 | 26% helix, 22% strand | P09148 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.90 | 0.91 | 128 | GDU, K |
| 2 | 782 | 0.87 | 0.90 | 83 | empty |
| 3 | 394 | 0.85 | 0.93 | 69 | K, GDU |
| 4 | 335 | 0.83 | 0.93 | 57 | GDU, K |
| 5 | 416 | 0.83 | 0.91 | 63 | GDU, K |
Interfaces
2 interfaces between chains.
- A–B · 3940 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3933 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 1GUP · Structure of nucleotidyltransferase complexed with udp-galactose · the same entry in another collection · chain D against D, TM-score 1.00
- P09148 · AlphaFold monomer V2.0 prediction for galactose-1-phosphate uridylyltransferase (P09148) · a predicted model of the same protein · 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 P09148
- Elsewhere: RCSB PDB 1GUP · PDBe 1GUP · UniProt P09148
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