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Structure of mycobacterium smegmatis succinate dehydrogenase 2

Analyse Structure of mycobacterium smegmatis succinate dehydrogenase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LUM
Type: protein
Length: 3,178 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinate dehydrogenase subunit C; Succinate dehydrogenase subunit D; Succinate…
Ligands: PEV, HEM, MQ9, CDL, LPP, PIE, FAD, FES, SF4, F3S
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 11 distinct chains · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Succinate dehydrogenase subunit C	protein	122	81% helix, 1% strand	—
D	Succinate dehydrogenase subunit D	protein	146	68% helix, 0% strand	—
E, I, O	Succinate dehydrogenase subunit F	protein	31	87% helix, 3% strand	—
A, P	Succinate dehydrogenase subunit a	protein	539	35% helix, 19% strand	—
B, Q	Succinate dehydrogenase subunit B	protein	238	32% helix, 11% strand	—
G	Succinate dehydrogenase subunit C	protein	123	84% helix, 1% strand	—
H	Succinate dehydrogenase subunit D	protein	120	80% helix, 0% strand	—
J	Succinate dehydrogenase subunit a	protein	534	32% helix, 17% strand	—
K	Succinate dehydrogenase subunit B	protein	247	30% helix, 11% strand	—
M	Succinate dehydrogenase subunit C	protein	123	80% helix, 1% strand	—
N	Succinate dehydrogenase subunit D	protein	116	83% helix, 0% strand	—

Ligands and binding sites

PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 6 copies · chains C, D, B, N, E, G, I, H, K, M, O, Q
HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains C, D, B, G, H, K, M, N, Q
MQ9 · Menaquinone-9 · ligand · 6 copies · chains D, H, N
CDL · Cardiolipin · ligand · 3 copies · chains C, D, E, H, G, I, N, M, O
LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 3 copies · chains D, M, N, O, C, E, H, G, I
PIE · 1,2-diacyl-sn-glycero-3-phosphoinositol · ligand · 3 copies · chains C, D, E, G, H, I, M, N, O
FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, J, P
FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, K, Q
SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, K, Q
F3S · FE3-S4 cluster · ligand · 3 copies · chains B, K, Q

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	1112	0.90	0.92	126	HEM
2	1189	0.89	0.91	118	HEM
3	1086	0.87	0.88	109	HEM
4	1078	0.86	0.87	148	FAD
5	1150	0.83	0.84	141	FAD

Interfaces

39 interfaces between chains.

J–K · 2619 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2380 Å² buried · 34 hydrogen bonds · protein-protein
P–Q · 2276 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 1879 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1858 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 7 covalent (covalent ligand, heme attachment, flavinylation).

Compared structures

6LUM · Structure of Mycobacterium smegmatis succinate dehydrogenase 2 · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6LUM · PDBe 6LUM

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