MolNFT v1 · #9940 · protein
Phosphoribosyldiphosphate synthetase in complex with cadmium ions
1IBS · Ribose-phosphate pyrophosphokinase: “Phosphoribosyldiphosphate synthetase in complex with cadmium ions”. X-ray diffraction, 3 ligands (ABM, CD, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #9940 on GenesisL1: 3D structure…
- PDB
- 1IBS
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- P14193
- Ligands
- ABM, CD, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 297 | 33% helix, 24% strand | P14193 |
| B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 299 | 32% helix, 22% strand | P14193 |
Ligands and binding sites
- ABM · Methyl phosphonic acid adenosine ester · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.75 | 0.79 | 82 | SO4, CD |
| 2 | 101 | 0.37 | 0.74 | 25 | empty |
| 3 | 73 | 0.36 | 0.77 | 14 | SO4, CD |
| 4 | 85 | 0.34 | 0.75 | 20 | empty |
| 5 | 70 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1431 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1IBS · Phosphoribosyldiphosphate synthetase in complex with cadmium ions · the same entry in another collection · chain A against A, TM-score 1.00
- P14193 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (P14193) · 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 P14193
- Elsewhere: RCSB PDB 1IBS · PDBe 1IBS · UniProt P14193
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