MolNFT v1 · #5670 · protein
Crystal structure of lactococcus lactis dihydroorotate dehydrogenase B. data collected under cryogenic conditions.
1EP3 · Dihydroorotate dehydrogenase B (pyrd subunit): “Crystal structure of lactococcus lactis dihydroorotate dehydrogenase B. data collected under cryogenic…”. X-ray diffraction, 3 ligands (FMN, FAD, FES), 6 pockets (best druggability…
- PDB
- 1EP3
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase B (pyrd subunit); Dihydroorotate dehydrogenase B (pyrk…
- EC
- 1.3.3.1
- UniProt
- P54322, P56968
- Ligands
- FMN, FAD, FES
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase B (pyrd subunit) (EC 1.3.3.1) | protein | 311 | 37% helix, 21% strand | P54322 |
| B | Dihydroorotate dehydrogenase B (pyrk subunit) (EC 1.3.3.1) | protein | 261 | 20% helix, 37% strand | P56968 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains 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 | 521 | 0.78 | 0.85 | 76 | FMN |
| 2 | 760 | 0.73 | 0.78 | 75 | FAD |
| 3 | 129 | 0.52 | 0.81 | 23 | empty |
| 4 | 88 | 0.43 | 0.79 | 22 | empty |
| 5 | 88 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1266 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1EP3 · Crystal structure of lactococcus lactis dihydroorotate dehydrogenase B. data collected… · the same entry in another collection · chain A against A, TM-score 1.00
- P54322 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase B (NAD(+)), catalytic… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P56968 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase B (NAD(+)), electron… · 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 P54322
- Every structure of UniProt P56968
- Elsewhere: RCSB PDB 1EP3 · PDBe 1EP3 · UniProt P54322 · UniProt P56968
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