MolNFT v1 · #38497 · protein
Crystal structure of human phosphoribosyl pyrophosphate synthetase 1
2H06 · Ribose-phosphate pyrophosphokinase I: “Crystal structure of human phosphoribosyl pyrophosphate synthetase 1”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.81). MolNFT v1 #38497 on GenesisL1: 3D structure…
- PDB
- 2H06
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase I
- EC
- 2.7.6.1
- UniProt
- P60891
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) | protein | 305 | 36% helix, 28% strand | P60891 |
| B | Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) | protein | 308 | 37% helix, 26% strand | P60891 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.81 | 0.83 | 82 | SO4 |
| 2 | 173 | 0.59 | 0.82 | 26 | empty |
| 3 | 151 | 0.59 | 0.83 | 28 | empty |
| 4 | 109 | 0.38 | 0.75 | 27 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1742 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2H06 · Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P60891 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase 1 (P60891) · a predicted model of the same protein · chain B 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 P60891
- Elsewhere: RCSB PDB 2H06 · PDBe 2H06 · UniProt P60891
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