MolNFT v1 · #177591 · protein

Iron and alpha-ketoglutarate-dependent endoperoxidase nvfi with different conformation

7ENB: “Iron and alpha-ketoglutarate-dependent endoperoxidase nvfi with different conformation”. X-ray diffraction, 3 ligands (OGA, H3X, FE), 5 pockets (best druggability 0.78). MolNFT v1 #177591 on GenesisL1: 3D structure, binding sites…

PDB: 7ENB
Type: protein
Length: 548 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nvfi
Ligands: OGA, H3X, FE
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nvfi	protein	277	22% helix, 35% strand	—
B	Nvfi	protein	271	23% helix, 33% strand	—

Ligands and binding sites

OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
H3X · Methyl (3'~{A}~{R},4'~{S},5'~{S},5~{A}~{S},6~{S},7~{S}, 9~{A}~{R})-1,1,3'~{A},4',5~{A},7,7'-heptamethyl-3,6'-bis(oxidanylidene)spiro[4,5,7,8,9,9~{a}-hexahydrobenzo[c]oxepine-6,2'-4,5-dihydro-3~{H}-1-benzofuran]-5'-carboxylate · ligand · chains A
FE · Fe (III) ion · metal · 2 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.78	0.87	45	H3X, OGA, FE
2	684	0.76	0.82	80	empty
3	363	0.73	0.84	37	OGA, FE
4	144	0.51	0.79	22	empty
5	65	0.32	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 784 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7ENB · iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation · 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
Elsewhere: RCSB PDB 7ENB · PDBe 7ENB

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