MolNFT v1 · #38750 · protein

Avian mitochondrial respiratory complex II at 1.8 ångström resolution

2H88 · Succinate dehydrogenase flavoprotein subunit: “Avian mitochondrial respiratory complex II at 1.8 ångström resolution”. X-ray diffraction, 10 ligands (FAD, TEO, FES), 20 pockets (best druggability 0.86). MolNFT v1 #38750 on…

PDB: 2H88
Type: protein
Length: 2,182 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinate dehydrogenase flavoprotein subunit; Succinate dehydrogenase ip subunit…
EC: 1.3.5.1
UniProt: Q9YHT1, Q9YHT2, Q5ZIS0
Ligands: FAD, TEO, FES, SF4, F3S, BHG, HEM, K, UNL, AZI
Pockets: 20 · best druggability 0.86

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1)	protein	612	35% helix, 23% strand	Q9YHT1
B, O	Succinate dehydrogenase ip subunit (EC 1.3.5.1)	protein	239	33% helix, 15% strand	Q9YHT2
C, P	Succinate dehydrogenase cytochrome B, large subunit (EC 1.3.5.1)	protein	139	75% helix, 1% strand	—
D, Q	Succinate dehydrogenase cytochrome B, small subunit (EC 1.3.5.1)	protein	101	87% helix, 0% strand	Q5ZIS0

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, N, O
TEO · Malate like intermediate · ligand · 2 copies · chains A, N
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, O
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, O
F3S · FE3-S4 cluster · ligand · 2 copies · chains B, O
BHG · hexyl beta-D-galactopyranoside · ligand · 2 copies · chains B, C, P, O
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, O, P, Q
K · Potassium ion · metal · 4 copies · chains A, B, N, O
UNL · Unknown ligand · ion · 64 copies · chains A, B, C, D, N, O, P, Q
AZI · Azide ion · ion · 2 copies · chains A, B, N, O
GOL · Glycerol · additive · 2 copies · chains B, C, O, P

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	328	0.86	0.96	60	FAD, TEO
2	318	0.86	0.96	56	FAD, TEO
3	1115	0.84	0.84	92	UNL, HEM
4	1188	0.83	0.84	98	UNL, HEM
5	457	0.79	0.87	46	empty

Interfaces

15 interfaces between chains.

N–O · 2716 Å² buried · 51 hydrogen bonds · protein-protein
A–B · 2711 Å² buried · 51 hydrogen bonds · protein-protein
O–P · 1822 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1822 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1366 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (flavinylation).

Compared structures

2H88 · Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution · the same entry in another collection · chain Q against Q, TM-score 1.00
Q9YHT1 · 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
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 Q9YHT1
Every structure of UniProt Q9YHT2
Every structure of UniProt Q5ZIS0
Elsewhere: RCSB PDB 2H88 · PDBe 2H88 · UniProt Q9YHT1 · UniProt Q9YHT2 · UniProt Q5ZIS0

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