MolNFT v1 · #11595 · protein

The P56A mutant of lactococcus lactis dihydroorotate dehydrogenase a

1JRB: “The P56A mutant of lactococcus lactis dihydroorotate dehydrogenase a”. X-ray diffraction, 2 ligands (FMN, ORO), 4 pockets (best druggability 0.77). MolNFT v1 #11595 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JRB
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
Pockets: 4 · best druggability 0.77

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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	568	0.77	0.84	90	FMN, ORO
2	489	0.77	0.85	81	FMN, ORO
3	122	0.55	0.82	19	empty
4	52	0.36	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 2309 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

1JRB · The P56A 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 1JRB · PDBe 1JRB · UniProt P54321

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