MolNFT v1 · #135855 · protein
Catalytic core domain of adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni with bound prpp
5UBI · ATP phosphoribosyltransferase: “Catalytic core domain of adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni with…”. X-ray diffraction, 3 ligands (PRP, ZN, MG), 1 pocket (best druggability 0.81). MolNFT v1…
- PDB
- 5UBI
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q5HSJ4
- Ligands
- PRP, ZN, MG
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 218 | 33% helix, 28% strand | Q5HSJ4 |
| B | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 222 | 33% helix, 29% strand | Q5HSJ4 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.81 | 0.82 | 100 | ZN, ACT, PRP, MG |
Interfaces
1 interface between chains.
- A–B · 1321 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5UBI · Catalytic core domain of Adenosine triphosphate phosphoribosyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HSJ4 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q5HSJ4) · 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 Q5HSJ4
- Elsewhere: RCSB PDB 5UBI · PDBe 5UBI · UniProt Q5HSJ4
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