Research workbench
Crystal structure of a putative udp-glucose pyrophosphorylase from arabidopsis thaliana with bound UTP
Analyse Crystal structure of a putative udp-glucose pyrophosphorylase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ICX
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable UTP-glucose-1-phosphate uridylyltransferase 2
- EC
- 2.7.7.9
- UniProt
- Q9M9P3
- Ligands
- UTP
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable UTP-glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) | protein | 455 | 33% helix, 28% strand | Q9M9P3 |
| B | Probable UTP-glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) | protein | 459 | 34% helix, 27% strand | Q9M9P3 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.75 | 0.81 | 54 | UTP |
| 2 | 354 | 0.69 | 0.82 | 42 | empty |
| 3 | 583 | 0.64 | 0.76 | 49 | UTP |
| 4 | 162 | 0.63 | 0.85 | 24 | empty |
| 5 | 144 | 0.63 | 0.86 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2ICX · Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9M9P3 · AlphaFold monomer V2.0 prediction for UTP--glucose-1-phosphate uridylyltransferase 2… · 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 Q9M9P3
- Elsewhere: RCSB PDB 2ICX · PDBe 2ICX · UniProt Q9M9P3
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