Research workbench
Crystal structure of orotate phosphoribosyltransferase from aeropyrum pernix
Analyse Crystal structure of orotate phosphoribosyltransferase from aeropyrum pernix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZK
- Type
- protein
- Length
- 687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- Q9Y9D8
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 177 | 39% helix, 28% strand | Q9Y9D8 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 167 | 42% helix, 29% strand | Q9Y9D8 |
| C | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 166 | 43% helix, 30% strand | Q9Y9D8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
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 | 1123 | 0.82 | 0.84 | 105 | PO4 |
| 2 | 316 | 0.54 | 0.75 | 35 | empty |
| 3 | 223 | 0.50 | 0.76 | 28 | PO4 |
| 4 | 76 | 0.37 | 0.77 | 19 | empty |
| 5 | 52 | 0.31 | 0.77 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1292 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1273 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2YZK · Crystal structure of orotate phosphoribosyltransferase from Aeropyrum pernix · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y9D8 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (Q9Y9D8) · 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 Q9Y9D8
- Elsewhere: RCSB PDB 2YZK · PDBe 2YZK · UniProt Q9Y9D8
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