Research workbench
Crystal structure of the putative dihydroorotate dehydrogenase from streptococcus mutans
Analyse Crystal structure of the putative dihydroorotate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OIX
- Type
- protein
- Length
- 1,239 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dihydroorotate dehydrogenase
- EC
- 1.3.3.1, 1.3.5.2
- UniProt
- Q8DVA1
- Ligands
- FMN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative dihydroorotate dehydrogenase (EC 1.3.3.1, 1.3.5.2) | protein | 310 | 37% helix, 21% strand | Q8DVA1 |
| D | Putative dihydroorotate dehydrogenase (EC 1.3.3.1, 1.3.5.2) | protein | 309 | 38% helix, 21% strand | Q8DVA1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.80 | 0.85 | 68 | FMN |
| 2 | 621 | 0.80 | 0.85 | 71 | FMN |
| 3 | 809 | 0.80 | 0.83 | 91 | FMN |
| 4 | 675 | 0.79 | 0.84 | 59 | FMN |
| 5 | 224 | 0.60 | 0.80 | 29 | GOL |
Interfaces
3 interfaces between chains.
- C–D · 2284 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2280 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 249 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (methylation).
Compared structures
- 3OIX · Crystal structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8DVA1
- Elsewhere: RCSB PDB 3OIX · PDBe 3OIX · UniProt Q8DVA1
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