MolNFT v1 · #190617 · protein
E.COLI phosphoribosylpyrophosphate (prpp) synthetase type B filament bound with pi
7XN3 · Ribose-phosphate pyrophosphokinase: “E.COLI phosphoribosylpyrophosphate (prpp) synthetase type B filament bound with pi”. Electron microscopy, 1 ligand (PO4), 14 pockets (best druggability 0.83). MolNFT v1 #190617 on GenesisL1: 3D…
- PDB
- 7XN3
- Type
- protein
- Length
- 1,830 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
- PO4
- Pockets
- 14 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, E, C, D | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 305 | 32% helix, 25% strand | P0A717 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, F, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.83 | 0.85 | 102 | PO4 |
| 2 | 841 | 0.82 | 0.85 | 85 | PO4 |
| 3 | 877 | 0.82 | 0.84 | 95 | PO4 |
| 4 | 634 | 0.82 | 0.87 | 63 | PO4 |
| 5 | 615 | 0.81 | 0.86 | 62 | PO4 |
Interfaces
12 interfaces between chains.
- B–C · 2043 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 2026 Ų buried · 28 hydrogen bonds · protein-protein
- E–D · 2022 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 925 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7XN3 · E.coli phosphoribosylpyrophosphate (PRPP) synthetase type B filament bound with Pi · the same entry in another collection · chain F against F, 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 0.97
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 7XN3 · PDBe 7XN3 · UniProt P0A717
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