MolNFT v1 · #41041 · protein
Human phosphoribosyl transferase domain containing 1
2JBH · Phosphoribosyltransferase domain-containing protein 1: “Human phosphoribosyl transferase domain containing 1”. X-ray diffraction, 3 ligands (5GP, CA, PO4), 5 pockets (best druggability 0.59). MolNFT v1 #41041 on GenesisL1: 3D…
- PDB
- 2JBH
- Type
- protein
- Length
- 421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyltransferase domain-containing protein 1
- EC
- 2.4.2.8
- UniProt
- Q9NRG1
- Ligands
- 5GP, CA, PO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyltransferase domain-containing protein 1 (EC 2.4.2.8) | protein | 208 | 32% helix, 29% strand | Q9NRG1 |
| B | Phosphoribosyltransferase domain-containing protein 1 (EC 2.4.2.8) | protein | 213 | 31% helix, 34% strand | Q9NRG1 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.59 | 0.77 | 39 | empty |
| 2 | 237 | 0.51 | 0.76 | 28 | PO4, CA, 5GP |
| 3 | 162 | 0.43 | 0.74 | 23 | PO4, CA, 5GP |
| 4 | 88 | 0.37 | 0.76 | 20 | empty |
| 5 | 81 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1185 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 2JBH · Human phosphoribosyl transferase domain containing 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRG1 · AlphaFold monomer V2.0 prediction for phosphoribosyltransferase domain-containing protein… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9NRG1
- Elsewhere: RCSB PDB 2JBH · PDBe 2JBH · UniProt Q9NRG1
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