Research workbench
Adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni in complex with the inhibitors AMP and histidine
Analyse Adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YB6
- Type
- protein
- Length
- 1,758 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q5HSJ4
- Ligands
- AMP, HIS, MG
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 296 | 35% helix, 34% strand | Q5HSJ4 |
| B | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 290 | 34% helix, 34% strand | Q5HSJ4 |
| C, D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 295 | 34% helix, 34% strand | Q5HSJ4 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 293 | 35% helix, 34% strand | Q5HSJ4 |
| F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 289 | 34% helix, 35% strand | Q5HSJ4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 6 copies · chains A, D, B, C, E, F
- HIS · Histidine · ligand · 6 copies · chains A, E, B, C, F, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.76 | 0.79 | 108 | AMP, MG |
| 2 | 877 | 0.75 | 0.79 | 87 | MG, AMP |
| 3 | 497 | 0.73 | 0.82 | 52 | MG |
| 4 | 690 | 0.63 | 0.74 | 80 | MG |
| 5 | 310 | 0.63 | 0.79 | 39 | AMP |
Interfaces
12 interfaces between chains.
- A–E · 1338 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1322 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1318 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 1308 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1307 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4YB6 · Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- Q5HSJ4 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q5HSJ4) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 4YB6 · PDBe 4YB6 · UniProt Q5HSJ4
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