Research workbench

Avian mitochondrial complex II with ttfa (thenoyltrifluoroacetone) bound

Analyse Avian mitochondrial complex II with ttfa (thenoyltrifluoroacetone) bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MYP
Type: protein
Length: 1,093 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, BCT, FES, SF4, F3S, TTF, HEM, UMQ, 3PE, K, MG
Pockets: 15 · best druggability 0.84

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	612	33% helix, 22% 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 · 63 copies · chains A, B, C, D
FAD · Flavin-adenine dinucleotide · ligand · chains A
OAA · Oxaloacetate ion · ligand · chains A
BCT · Bicarbonate 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
TTF · 4,4,4-trifluoro-1-thien-2-ylbutane-1,3-dione · 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
MG · Magnesium 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

15 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	306	0.84	0.95	57	FAD, OAA
2	1196	0.83	0.84	102	TTF, HEM, UNL, 3PE
3	111	0.77	0.97	31	UNL
4	332	0.74	0.85	34	UNL
5	438	0.68	0.80	38	PEG, UNL

Interfaces

5 interfaces between chains.

A–B · 2677 Å² buried · 50 hydrogen bonds · protein-protein
B–C · 1799 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1352 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 638 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 131 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6MYP · Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound · 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 6MYP · PDBe 6MYP · UniProt F1NPJ4 · UniProt Q9YHT2 · UniProt D0VWW3 · UniProt Q5ZIS0

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