MolNFT v1 · #110923 · protein
Adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni in complex with ATP
4YB7 · ATP phosphoribosyltransferase: “Adenosine triphosphate phosphoribosyltransferase from campylobacter jejuni in complex with ATP”. X-ray diffraction, 3 ligands (ATP, MG, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #110923 on…
- PDB
- 4YB7
- Type
- protein
- Length
- 3,531 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q5HSJ4
- Ligands
- ATP, MG, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, H, J | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 296 | 32% helix, 33% strand | Q5HSJ4 |
| C | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 294 | 32% helix, 32% strand | Q5HSJ4 |
| D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 294 | 32% helix, 32% strand | Q5HSJ4 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 295 | 32% helix, 34% strand | Q5HSJ4 |
| I | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 292 | 32% helix, 34% strand | Q5HSJ4 |
| K | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 294 | 32% helix, 33% strand | Q5HSJ4 |
| F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 293 | 32% helix, 32% strand | Q5HSJ4 |
| G | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 292 | 33% helix, 33% strand | Q5HSJ4 |
| L | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 293 | 32% helix, 33% strand | Q5HSJ4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains B, C, D, E, I, K, A, F, G, H, J, L
- MG · Magnesium ion · metal · 12 copies · chains B, C, D, E, I, K, A, F, G, H, J, L
- PO4 · Phosphate ion · ion · 6 copies · chains B, C, E, I, J
- ACY · Acetic acid · additive · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.82 | 0.83 | 112 | empty |
| 2 | 754 | 0.79 | 0.82 | 88 | empty |
| 3 | 710 | 0.77 | 0.82 | 91 | empty |
| 4 | 704 | 0.76 | 0.81 | 89 | empty |
| 5 | 1066 | 0.74 | 0.77 | 105 | MG, PO4, ATP |
Interfaces
25 interfaces between chains.
- D–I · 1093 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1089 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 1082 Ų buried · 21 hydrogen bonds · protein-protein
- E–K · 986 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 974 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4YB7 · Adenosine triphosphate phosphoribosyltransferase from Campylobacter jejuni in complex… · the same entry in another collection · chain K against K, TM-score 1.00
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 4YB7 · PDBe 4YB7 · UniProt Q5HSJ4
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