MolNFT v1 · #38894 · protein
Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and sulfate ion
2HCR · Ribose-phosphate pyrophosphokinase I: “Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with AMP(ATP), cadmium and…”. X-ray diffraction, 3 ligands (AMP, CD, SO4), 5 pockets (best druggability 0.81).…
- PDB
- 2HCR
- 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
- AMP, CD, SO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) | protein | 305 | 35% helix, 25% strand | P60891 |
| B | Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) | protein | 308 | 37% helix, 25% strand | P60891 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.81 | 0.82 | 95 | SO4, CD |
| 2 | 246 | 0.65 | 0.83 | 44 | empty |
| 3 | 188 | 0.60 | 0.82 | 25 | empty |
| 4 | 79 | 0.36 | 0.76 | 18 | SO4 |
| 5 | 69 | 0.34 | 0.76 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1738 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2HCR · crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in complex with… · 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 2HCR · PDBe 2HCR · UniProt P60891
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