Research workbench
Adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni in complex with the allosteric inhibitor 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
- 4YB5
- Type
- protein
- Length
- 1,753 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
- HIS, K, SCN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 291 | 34% helix, 34% strand | Q5HSJ4 |
| B, C | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 295 | 33% helix, 34% strand | Q5HSJ4 |
| D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 292 | 34% helix, 34% strand | Q5HSJ4 |
| E, F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 290 | 34% helix, 34% strand | Q5HSJ4 |
Ligands and binding sites
- HIS · Histidine · ligand · 6 copies · chains A, E, B, C, F, D
- K · Potassium ion · metal · 5 copies · chains A, F, B, D, C, E
- SCN · Thiocyanate ion · ion · 8 copies · chains A, F, B, C, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D, F
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.82 | 0.84 | 99 | empty |
| 2 | 549 | 0.81 | 0.87 | 53 | empty |
| 3 | 514 | 0.81 | 0.88 | 51 | empty |
| 4 | 273 | 0.68 | 0.83 | 47 | empty |
| 5 | 248 | 0.68 | 0.84 | 41 | empty |
Interfaces
15 interfaces between chains.
- B–F · 1316 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1307 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1307 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1306 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1302 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4YB5 · 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 0.93
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 4YB5 · PDBe 4YB5 · UniProt Q5HSJ4
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