MolNFT v1 · #111532 · protein

Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris suum with N-biphenyl-3-yl-2-(TRIFLUOROMETHYL)BENZAMIDE

4YTM · Succinate dehydrogenase flavoprotein: “Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris suum with…”. X-ray diffraction, 7 ligands (FAD, FES, SF4), 20 pockets (best druggability 0.86). MolNFT v1 #111532…

PDB: 4YTM
Type: protein
Length: 2,295 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinate dehydrogenase flavoprotein; Succinate dehydrogenase [ubiquinone] iron-sulfur…
EC: 1.3.5.1
UniProt: U1LRQ3, O44074, P92506, P92507
Ligands: FAD, FES, SF4, F3S, HEM, F6A, EPH
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Succinate dehydrogenase flavoprotein	protein	616	33% helix, 21% strand	U1LRQ3
B	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1)	protein	250	28% helix, 14% strand	O44074
C	Cytochrome B-large subunit	protein	152	74% helix, 1% strand	P92506
D, H	Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial	protein	129	69% helix, 2% strand	P92507
F	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1)	protein	252	28% helix, 13% strand	O44074
G	Cytochrome B-large subunit	protein	151	74% helix, 1% strand	P92506

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, E, F
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, F
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, F
F3S · FE3-S4 cluster · ligand · 2 copies · chains B, F
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, F, G, H
F6A · N-biphenyl-3-yl-2-(trifluoromethyl)benzamide · ligand · 2 copies · chains B, C, D, F, G, H
EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains C, D
MLI · Malonate ion · additive · 2 copies · chains A, E

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1106	0.86	0.87	89	HEM, F6A
2	1064	0.86	0.87	95	HEM, F6A, EPH
3	325	0.86	0.96	56	MLI, FAD
4	318	0.86	0.96	56	MLI, FAD
5	403	0.76	0.86	68	empty

Interfaces

18 interfaces between chains.

E–F · 2788 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2761 Å² buried · 39 hydrogen bonds · protein-protein
F–G · 1927 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1916 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1881 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4YTM · Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with… · the same entry in another collection · chain H against H, TM-score 1.00
P92507 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain H against A, TM-score 0.89

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 U1LRQ3
Every structure of UniProt O44074
Every structure of UniProt P92506
Every structure of UniProt P92507
Elsewhere: RCSB PDB 4YTM · PDBe 4YTM · UniProt U1LRQ3 · UniProt O44074 · UniProt P92506 · UniProt P92507

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