MolNFT v1 · #190616 · protein
E.COLI phosphoribosylpyrophosphate (prpp) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P
7XMV · Ribose-phosphate pyrophosphokinase: “E.COLI phosphoribosylpyrophosphate (prpp) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P”. Electron microscopy, 4 ligands (HSX, ADP, AMP), 20 pockets (best druggability 0.78).…
- PDB
- 7XMV
- Type
- protein
- Length
- 1,842 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- P0A717
- Ligands
- HSX, ADP, AMP, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C, D, B, F | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 307 | 35% helix, 23% strand | P0A717 |
Ligands and binding sites
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 6 copies · chains A, E, C, D, B, F
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, F, E, B, C, D
- AMP · Adenosine monophosphate · ligand · 6 copies · chains A, C, E, F, D, B
- MG · Magnesium ion · metal · 12 copies · chains A, E, C, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.78 | 0.80 | 104 | HSX, MG, AMP |
| 2 | 935 | 0.77 | 0.80 | 96 | HSX, MG, AMP |
| 3 | 1146 | 0.76 | 0.78 | 102 | HSX, MG, AMP |
| 4 | 124 | 0.37 | 0.74 | 20 | empty |
| 5 | 56 | 0.36 | 0.79 | 16 | ADP |
Interfaces
12 interfaces between chains.
- A–F · 1976 Ų buried · 20 hydrogen bonds · protein-protein
- E–B · 1974 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1970 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1848 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1836 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7XMV · E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/ADP) filament bound with… · the same entry in another collection · chain C against C, TM-score 1.00
- P0A717 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (P0A717) · 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 P0A717
- Elsewhere: RCSB PDB 7XMV · PDBe 7XMV · UniProt P0A717
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