MolNFT v1 · #53784 · protein

The crystal structure of MFE1 liganded with CoA

2X58 · Peroxisomal bifunctional enzyme: “The crystal structure of MFE1 liganded with CoA”. X-ray diffraction, 3 ligands (COA, ADP, SO4), 18 pockets (best druggability 0.78). MolNFT v1 #53784 on GenesisL1: 3D structure, binding sites and…

PDB: 2X58
Type: protein
Length: 1,446 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisomal bifunctional enzyme
EC: 4.2.1.17, 5.3.3.8, 1.1.1.35
UniProt: P07896
Ligands: COA, ADP, SO4
Pockets: 18 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisomal bifunctional enzyme (EC 4.2.1.17, 5.3.3.8, 1.1.1.35)	protein	725	50% helix, 13% strand	P07896
B	Peroxisomal bifunctional enzyme (EC 4.2.1.17, 5.3.3.8, 1.1.1.35)	protein	721	50% helix, 13% strand	P07896

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

18 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	1149	0.78	0.80	103	ADP
2	601	0.74	0.81	67	SO4
3	412	0.71	0.82	39	empty
4	364	0.64	0.79	60	COA, GOL
5	235	0.63	0.82	44	COA, GOL

Interfaces

1 interface between chains.

A–B · 868 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2X58 · The crystal structure of MFE1 liganded with CoA · the same entry in another collection · chain A against A, TM-score 1.00
P07896 · AlphaFold monomer V2.0 prediction for peroxisomal bifunctional enzyme (P07896) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P07896
Elsewhere: RCSB PDB 2X58 · PDBe 2X58 · UniProt P07896

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