8OVD: Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis

PDB ID: 8OVDDownload
MMDB ID: 249826
PDB Deposition Date: 2023/4/25
Updated in MMDB: 2024/07
Experimental Method:
electron microscopy
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 8OVD: 24-meric; determined by author and by software (PISA)
Molecular Components in 8OVD
Label Count Molecule
Proteins (24 molecules)
2
Cytochrome BC1 Complex Cytochrome C Subunit
Molecule annotation
2
Cytochrome BC1 Complex Cytochrome C Subunit
Molecule annotation
2
Cytochrome BC1 Complex Cytochrome B Subunit
Molecule annotation
2
Transmembrane Protein
Molecule annotation
2
Probable Cytochrome C Oxidase Subunit 3
Molecule annotation
2
Cytochrome C Oxidase Polypeptide 4
Molecule annotation
2
Cytochrome C Oxidase Subunit 1
Molecule annotation
2
Cytochrome-c Oxidase
Molecule annotation
2
Cytochrome C Oxidase Subunit
Molecule annotation
2
Uncharacterized Protein Msmeg_4692/msmei_4575
Molecule annotation
2
Lpqe Protein
Molecule annotation
2
Superoxide Dismutase [cu-zn]
Molecule annotation
Chemicals and Non-standard biopolymers (86 molecules)
1
4
HEME CHEME C
2
12
MENAQUINONE-9MENAQUINONE-9
3
4
acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
4
2
FE2/S2 (INORGANIC) CLUSTERFE2/S2 (INORGANIC) CLUSTER
5
2
[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate
6
4
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
7
5
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
8
4
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
9
15
CARDIOLIPINCARDIOLIPIN
10
10
TRIDECANETRIDECANE
11
2
1,2-Distearoyl-sn-glycerophosphoethanolamine1,2-Distearoyl-sn-glycerophosphoethanolamine
12
4
HEME-AHEME-A
13
6
COPPER (II) IONCOPPER (II) ION
14
2
MAGNESIUM IONMAGNESIUM ION
15
2
CALCIUM IONCALCIUM ION
16
4
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
17
4
PALMITIC ACIDPALMITIC ACID
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303