Research workbench
ATP phosphoribosyltransferase (hiszg atpprt) from psychrobacter arcticus in complex with prpp and ADP
Analyse ATP phosphoribosyltransferase (hiszg atpprt) from psychrobacter arcticus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FUA
- Type
- protein
- Length
- 1,161 residues
- Chains
- 4
- 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
- ADP, PRP, MG, CL
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase regulatory subunit | protein | 375 | 40% helix, 22% strand | Q4FTX3 |
| B | ATP phosphoribosyltransferase regulatory subunit | protein | 377 | 42% helix, 22% strand | Q4FTX3 |
| C | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 205 | 31% helix, 33% strand | Q4FQF7 |
| D | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 204 | 32% helix, 33% strand | Q4FQF7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.82 | 0.83 | 131 | CL |
| 2 | 804 | 0.79 | 0.83 | 96 | CL |
| 3 | 1013 | 0.76 | 0.78 | 96 | ADP, MG |
| 4 | 57 | 0.73 | 0.99 | 17 | empty |
| 5 | 52 | 0.73 | 1.00 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3230 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 668 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FUA · ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q4FQF7 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q4FQF7) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q4FTX3 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase regulatory subunit… · a predicted model of the same protein · chain B 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 Q4FTX3
- Every structure of UniProt Q4FQF7
- Elsewhere: RCSB PDB 6FUA · PDBe 6FUA · UniProt Q4FTX3 · UniProt Q4FQF7
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