Research workbench
Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and prpp
Analyse Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and prpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R02
- Type
- protein
- Length
- 2,326 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
- Q4FTX3, Q4FQF7
- Ligands
- HIS, PRP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | ATP phosphoribosyltransferase regulatory subunit | protein | 378 | 40% helix, 21% strand | Q4FTX3 |
| C | ATP phosphoribosyltransferase regulatory subunit | protein | 379 | 41% helix, 21% strand | Q4FTX3 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 202 | 32% helix, 33% strand | Q4FQF7 |
| F | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 200 | 31% helix, 36% strand | Q4FQF7 |
| G | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 208 | 33% helix, 33% strand | Q4FQF7 |
| H | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 203 | 32% helix, 32% strand | Q4FQF7 |
Ligands and binding sites
- HIS · Histidine · ligand · 4 copies · chains A, B, C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.85 | 0.87 | 135 | HIS |
| 2 | 962 | 0.82 | 0.84 | 107 | HIS |
| 3 | 868 | 0.80 | 0.83 | 65 | empty |
| 4 | 742 | 0.80 | 0.84 | 85 | HIS |
| 5 | 285 | 0.75 | 0.88 | 46 | HIS |
Interfaces
20 interfaces between chains.
- A–B · 3282 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3245 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 1163 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1074 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 935 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6R02 · Psychrobacter arcticus ATP phosphoribosyltransferase bound to histidine and PRPP · the same entry in another collection · chain G against G, TM-score 1.00
- Q4FQF7 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q4FQF7) · a predicted model of the same protein · chain E 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 Q4FTX3
- Every structure of UniProt Q4FQF7
- Elsewhere: RCSB PDB 6R02 · PDBe 6R02 · UniProt Q4FTX3 · UniProt Q4FQF7
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