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Crystal structure of porcine heart mitochondrial complex II with an empty quinone-binding pocket

Analyse Crystal structure of porcine heart mitochondrial complex II with an empty… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AEF
Type: protein
Length: 1,092 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
EC: 1.3.5.1
UniProt: Q0QF01, Q007T0, D0VWV4, A5GZW8
Ligands: FAD, FES, SF4, F3S, HEM, EPH
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1)	protein	613	35% helix, 22% strand	Q0QF01
B	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1)	protein	239	31% helix, 15% strand	Q007T0
C	Succinate dehydrogenase cytochrome B560 subunit, mitochondrial	protein	138	76% helix, 1% strand	D0VWV4
D	Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial	protein	102	86% helix, 0% strand	A5GZW8

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
FES · Fe2/s2 (inorganic) cluster · ligand · chains B
SF4 · Iron/sulfur cluster · ligand · chains B
F3S · FE3-S4 cluster · ligand · chains B
HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	316	0.86	0.97	53	FAD
2	1184	0.84	0.85	99	HEM, EPH
3	83	0.74	0.97	21	empty
4	366	0.70	0.82	32	empty
5	400	0.66	0.79	34	empty

Interfaces

5 interfaces between chains.

A–B · 2753 Å² buried · 55 hydrogen bonds · protein-protein
B–C · 1720 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1359 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 684 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 103 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor (flavinylation).

Compared structures

3AEF · Crystal structure of porcine heart mitochondrial complex II with an empty qui -binding… · the same entry in another collection · chain D against D, TM-score 1.00
Q0QF01 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] flavoprotein… · a predicted model of the same protein · chain A against A, TM-score 1.00
Q007T0 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain B against A, TM-score 0.99
A5GZW8 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.99
D0VWV4 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase cytochrome B560 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.93

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 Q0QF01
Every structure of UniProt Q007T0
Every structure of UniProt D0VWV4
Every structure of UniProt A5GZW8
Elsewhere: RCSB PDB 3AEF · PDBe 3AEF · UniProt Q0QF01 · UniProt Q007T0 · UniProt D0VWV4 · UniProt A5GZW8

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