Research workbench
Crystal structure of glucose-1-phosphate bound nucleotidylated human galactose-1-phosphate uridylyltransferase
Analyse Crystal structure of glucose-1-phosphate bound nucleotidylated human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IN3
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactose-1-phosphate uridylyltransferase
- EC
- 2.7.7.12
- UniProt
- P07902
- Ligands
- H2U, G1P, ZN
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) | protein | 330 | 29% helix, 21% strand | P07902 |
| A | Galactose-1-phosphate uridylyltransferase (EC 2.7.7.12) | protein | 324 | 29% helix, 21% strand | P07902 |
Ligands and binding sites
- H2U · 5,6-dihydrouridine-5'-monophosphate · ligand · 2 copies · chains B, A
- G1P · 1-O-phosphono-alpha-D-glucopyranose · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 28 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.86 | 0.90 | 64 | empty |
| 2 | 437 | 0.67 | 0.79 | 38 | H2U, EDO, G1P |
| 3 | 420 | 0.67 | 0.79 | 41 | EDO, G1P, H2U |
| 4 | 127 | 0.47 | 0.78 | 32 | empty |
| 5 | 93 | 0.45 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- B–A · 3320 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 5IN3 · Crystal structure of glucose-1-phosphate bound nucleotidylated human… · the same entry in another collection · chain B against B, TM-score 1.00
- P07902 · AlphaFold monomer V2.0 prediction for galactose-1-phosphate uridylyltransferase (P07902) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P07902
- Elsewhere: RCSB PDB 5IN3 · PDBe 5IN3 · UniProt P07902
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