Research workbench
Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with gmp (guanosine 5'- monophosphate) (orthorhombic 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
- 2JKZ
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- 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, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 201 | 34% helix, 25% strand | Q04178 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.78 | 0.80 | 87 | empty |
| 2 | 575 | 0.69 | 0.78 | 81 | 5GP, SO4 |
| 3 | 309 | 0.63 | 0.79 | 50 | 5GP, SO4 |
| 4 | 268 | 0.52 | 0.75 | 39 | 5GP, SO4 |
| 5 | 198 | 0.49 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1752 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1711 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2JKZ · Saccharomyces cerevisiae hypoxanthine-guanine phosphoribosyltransferase in complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- Q04178 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain A 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 Q04178
- Elsewhere: RCSB PDB 2JKZ · PDBe 2JKZ · UniProt Q04178
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