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Crystal structure of L. lactis dihydroorotate dehydrogense a in complex with 3,5-dihydroxybenzoate
Analyse Crystal structure of L. lactis dihydroorotate dehydrogense a in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BX7
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- EC
- 1.3.3.1
- UniProt
- P54321
- Ligands
- FMN, 34D, MG
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 311 | 37% helix, 20% strand | P54321 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- 34D · 3,5-dihydroxybenzoate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.76 | 0.87 | 60 | FMN, ACT |
| 2 | 340 | 0.76 | 0.87 | 61 | FMN, 34D |
| 3 | 95 | 0.55 | 0.84 | 17 | GOL |
| 4 | 54 | 0.34 | 0.78 | 21 | empty |
| 5 | 57 | 0.29 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2309 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2BX7 · Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with… · 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 P54321
- Elsewhere: RCSB PDB 2BX7 · PDBe 2BX7 · UniProt P54321
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