Research workbench
Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with gmp (guanosine 5'- monophosphate) (tetragonal crystal form)
Analyse Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JKY
- Type
- protein
- Length
- 409 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q04178
- Ligands
- 5GP, MG, SO4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 207 | 34% helix, 22% strand | Q04178 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 202 | 37% helix, 25% strand | Q04178 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.79 | 0.94 | 32 | 5GP, SO4, MG |
| 2 | 278 | 0.57 | 0.77 | 36 | empty |
| 3 | 73 | 0.48 | 0.83 | 21 | empty |
| 4 | 175 | 0.47 | 0.76 | 26 | 5GP, SO4 |
| 5 | 56 | 0.43 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1728 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2JKY · Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04178 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · 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 Q04178
- Elsewhere: RCSB PDB 2JKY · PDBe 2JKY · UniProt Q04178
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