Research workbench
Crystal structure of phosphoribosyl diphosphate synthase complexed with AMP and ribose 5-phosphate
Analyse Crystal structure of phosphoribosyl diphosphate synthase complexed with AMP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U9Z
- Type
- protein
- Length
- 1,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- Q58761
- Ligands
- R5P, AMP
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 274 | 35% helix, 25% strand | Q58761 |
Ligands and binding sites
- R5P · Ribose-5-phosphate · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.77 | 0.81 | 75 | empty |
| 2 | 776 | 0.77 | 0.81 | 70 | empty |
| 3 | 97 | 0.47 | 0.80 | 18 | empty |
| 4 | 108 | 0.45 | 0.78 | 18 | empty |
| 5 | 119 | 0.39 | 0.75 | 24 | R5P |
Interfaces
4 interfaces between chains.
- C–D · 1875 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1848 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1340 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1323 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1U9Z · Crystal Structure of Phosphoribosyl Diphosphate Synthase Complexed with AMP and Ribose… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58761 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (Q58761) · a predicted model of the same protein · chain A 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 Q58761
- Elsewhere: RCSB PDB 1U9Z · PDBe 1U9Z · UniProt Q58761
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