MolNFT v1 · #11579 · protein
The K213E mutant of lactococcus lactis dihydroorotate dehydrogenase a
1JQV: “The K213E mutant of lactococcus lactis dihydroorotate dehydrogenase a”. X-ray diffraction, 3 ligands (FMN, ORO, MG), 5 pockets (best druggability 0.79). MolNFT v1 #11579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JQV
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase a
- EC
- 1.3.3.1
- UniProt
- P54321
- Ligands
- FMN, ORO, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase a (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
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 4 copies · chains A, B
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 | 777 | 0.79 | 0.83 | 79 | FMN, ORO, ACY |
| 2 | 762 | 0.79 | 0.83 | 81 | FMN, ORO, ACY |
| 3 | 196 | 0.59 | 0.81 | 26 | empty |
| 4 | 54 | 0.40 | 0.82 | 14 | empty |
| 5 | 65 | 0.38 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2375 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1JQV · The K213E mutant of Lactococcus lactis Dihydroorotate dehydrogenase A · 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 1JQV · PDBe 1JQV · UniProt P54321
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