Research workbench
ATP phosphoribosyl transferase (hiszg ATP-prtase) from lactococcus lactis with bound prpp substrate
Analyse ATP phosphoribosyl transferase (hiszg ATP-prtase) from lactococcus lactis with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z7N
- Type
- protein
- Length
- 2,058 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase regulatory subunit; ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q02147, Q02129
- Ligands
- PRP, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase regulatory subunit | protein | 313 | 45% helix, 20% strand | Q02147 |
| B | ATP phosphoribosyltransferase regulatory subunit | protein | 318 | 43% helix, 20% strand | Q02147 |
| C | ATP phosphoribosyltransferase regulatory subunit | protein | 304 | 44% helix, 21% strand | Q02147 |
| D | ATP phosphoribosyltransferase regulatory subunit | protein | 312 | 44% helix, 21% strand | Q02147 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 203 | 32% helix, 25% strand | Q02129 |
| F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 205 | 33% helix, 27% strand | Q02129 |
| G | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 203 | 33% helix, 27% strand | Q02129 |
| H | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 200 | 32% helix, 28% strand | Q02129 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains E, F, G, H
- PO4 · Phosphate ion · ion · 2 copies · chains D, F, B, G
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 | 1106 | 0.87 | 0.88 | 103 | PO4 |
| 2 | 1171 | 0.86 | 0.87 | 109 | PO4 |
| 3 | 177 | 0.79 | 0.95 | 32 | empty |
| 4 | 880 | 0.79 | 0.82 | 97 | empty |
| 5 | 322 | 0.78 | 0.89 | 48 | empty |
Interfaces
19 interfaces between chains.
- C–D · 2167 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2145 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 1184 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1137 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1105 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1Z7N · ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis with bound PRPP… · the same entry in another collection · chain H against H, TM-score 1.00
- Q02129 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q02129) · a predicted model of the same protein · chain G against A, TM-score 0.98
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 Q02147
- Every structure of UniProt Q02129
- Elsewhere: RCSB PDB 1Z7N · PDBe 1Z7N · UniProt Q02147 · UniProt Q02129
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