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Glutamine phosphoribosylpyrophosphate (prpp) amidotransferase from B. subtilis complexed with ADP and gmp
Analyse Glutamine phosphoribosylpyrophosphate (prpp) amidotransferase from B. subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AO0
- Type
- protein
- Length
- 1,820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine phosphoribosylpyrophosphate amidotransferase
- EC
- 2.4.2.14
- UniProt
- P00497
- Ligands
- SF4, 5GP, ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamine phosphoribosylpyrophosphate amidotransferase (EC 2.4.2.14) | protein | 455 | 30% helix, 26% strand | P00497 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.88 | 0.89 | 133 | SF4, 5GP, ADP |
| 2 | 830 | 0.87 | 0.89 | 103 | SF4, 5GP, ADP |
| 3 | 208 | 0.73 | 0.89 | 39 | SF4, 5GP |
| 4 | 622 | 0.72 | 0.79 | 67 | empty |
| 5 | 592 | 0.71 | 0.79 | 69 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2314 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2292 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1024 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1AO0 · Glutamine phosphoribosylpyrophosphate (prpp) amidotransferase from B. subtilis complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P00497 · AlphaFold monomer V2.0 prediction for amidophosphoribosyltransferase (P00497) · a predicted model of the same protein · chain A 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 P00497
- Elsewhere: RCSB PDB 1AO0 · PDBe 1AO0 · UniProt P00497
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