MolNFT v1 · #17495 · protein

The K136E mutant of lactococcus lactis dihydroorotate dehydrogenase a in complex with orotate

1OVD: “The K136E mutant of lactococcus lactis dihydroorotate dehydrogenase a in complex with orotate”. X-ray diffraction, 3 ligands (FMN, ORO, MG), 8 pockets (best druggability 0.77). MolNFT v1 #17495 on GenesisL1: 3D structure, binding…

PDB: 1OVD
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: 8 · 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
MG · Magnesium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.77	0.89	50	FMN, ORO
2	337	0.76	0.87	63	FMN, ORO
3	108	0.55	0.84	18	empty
4	105	0.54	0.83	18	empty
5	102	0.54	0.83	18	GOL

Interfaces

1 interface between chains.

A–B · 2334 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

1OVD · The K136E mutant of lactococcus lactis dihydroorotate dehydrogenase 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 1OVD · PDBe 1OVD · UniProt P54321

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