Research workbench
Crystal structure of orotate phosphoribosyltransferase from streptococcus mutans
Analyse Crystal structure of orotate phosphoribosyltransferase from streptococcus mutans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DEZ
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotate phosphoribosyltransferase
- EC
- 2.4.2.10
- UniProt
- Q8DTV2
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 206 | 44% helix, 22% strand | Q8DTV2 |
| B | Orotate phosphoribosyltransferase (EC 2.4.2.10) | protein | 194 | 46% helix, 21% strand | Q8DTV2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.36 | 0.75 | 21 | SO4 |
| 2 | 108 | 0.36 | 0.74 | 29 | SO4 |
| 3 | 64 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1328 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3DEZ · Crystal structure of Orotate phosphoribosyltransferase from Streptococcus mutans · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DTV2 · AlphaFold monomer V2.0 prediction for orotate phosphoribosyltransferase (Q8DTV2) · 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 Q8DTV2
- Elsewhere: RCSB PDB 3DEZ · PDBe 3DEZ · UniProt Q8DTV2
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