Research workbench

Avian mitochondrial complex II with atpenin A5 bound, sidechain in pocket

Analyse Avian mitochondrial complex II with atpenin A5 bound, sidechain in pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYT
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: F1NPJ4, Q9YHT2, D0VWW3, Q5ZIS0
Ligands: UNL, FAD, OAA, FES, SF4, F3S, AT5, HEM, UMQ, 3PE, K
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1)	protein	611	34% helix, 23% strand	F1NPJ4
B	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1)	protein	240	31% helix, 15% strand	Q9YHT2
C	Succinate dehydrogenase cytochrome B, large subunit (EC 1.3.5.1)	protein	139	73% helix, 1% strand	D0VWW3
D	Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial	protein	102	86% helix, 0% strand	Q5ZIS0

Ligands and binding sites

UNL · Unknown ligand · ligand · 59 copies · chains A, B, C, D
FAD · Flavin-adenine dinucleotide · ligand · chains A, B
OAA · Oxaloacetate ion · 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
AT5 · 3-[(2S,4S,5R)-5,6-dichloro-2,4-dimethyl-1-oxohexyl]-4-hydroxy-5,6-dimethoxy-2(1H)-pyridinone · ligand · chains B, C, D
HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
UMQ · Undecyl-maltoside · ligand · chains B, C
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains C, D
K · Potassium ion · metal · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	980	0.86	0.87	93	AT5, HEM, UNL, 3PE
2	298	0.85	0.95	51	FAD, OAA, UNL
3	101	0.76	0.96	19	UNL
4	296	0.72	0.86	37	UNL
5	435	0.68	0.80	37	PEG, UNL

Interfaces

5 interfaces between chains.

A–B · 2668 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 1810 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1409 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 634 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 151 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor, 1 modified (flavinylation, methylation).

Compared structures

6MYT · Avian mitochondrial complex II with Atpenin A5 bound, sidechain in pocket · the same entry in another collection · chain A against A, TM-score 1.00
Q9YHT2 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain B against A, TM-score 1.00
Q5ZIS0 · 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

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 F1NPJ4
Every structure of UniProt Q9YHT2
Every structure of UniProt D0VWW3
Every structure of UniProt Q5ZIS0
Elsewhere: RCSB PDB 6MYT · PDBe 6MYT · UniProt F1NPJ4 · UniProt Q9YHT2 · UniProt D0VWW3 · UniProt Q5ZIS0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.