Research workbench
Human udp-glucose pyrophosphorylase isoform 1 in complex with udp- glucose
Analyse Human udp-glucose pyrophosphorylase isoform 1 in complex with udp- glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R7P
- Type
- protein
- Length
- 1,935 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- Q16851
- Ligands
- UPG, ZN, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 485 | 33% helix, 28% strand | Q16851 |
| D | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 480 | 30% helix, 29% strand | Q16851 |
Ligands and binding sites
- UPG · Uridine-5'-diphosphate-glucose · ligand · chains A
- ZN · Zinc ion · metal · 11 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, D, C, B
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 | 920 | 0.72 | 0.76 | 113 | UPG |
| 2 | 617 | 0.70 | 0.78 | 76 | empty |
| 3 | 76 | 0.66 | 0.92 | 18 | empty |
| 4 | 352 | 0.66 | 0.80 | 30 | empty |
| 5 | 299 | 0.65 | 0.81 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–D · 352 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 325 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 174 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 4R7P · Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose · the same entry in another collection · chain A against A, TM-score 1.00
- Q16851 · AlphaFold monomer V2.0 prediction for UTP--glucose-1-phosphate uridylyltransferase… · a predicted model of the same protein · chain A 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 Q16851
- Elsewhere: RCSB PDB 4R7P · PDBe 4R7P · UniProt Q16851
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