MolNFT v1 · #185586 · protein
III2-IV2 respiratory supercomplex from corynebacterium glutamicum
7Q21 · Co-purified unknown transmembrane helices built as polyala…: “III2-IV2 respiratory supercomplex from corynebacterium glutamicum”. Electron microscopy, 15 ligands (TRD, 7PH, CDL), 20 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 7Q21
- Type
- protein
- Length
- 5,813 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Co-purified unknown transmembrane helices built as polyala (ascd); Cytochrome C oxidase…
- EC
- 7.1.1.9, 7.1.1.8
- UniProt
- Q9AEL8, Q8NP09, Q8NNK3, Q8NNK2, Q79VD7, Q79VE8, Q8NMB4, Q79VE9, Q8NNK5, Q8NS61, Q8NSJ8
- Ligands
- TRD, 7PH, CDL, MQ9, 9XX, HAS, 9YF, PLM, HEM, HEC, TWT, FES, CU, MG, CA
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 16 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Co-purified unknown transmembrane helices built as polyala (ascd) | protein | 96 | 39% helix, 0% strand | — |
| E, e | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 189 | 82% helix, 1% strand | Q9AEL8 |
| H | Uncharacterized membrane protein CGL2017/CG2211 | protein | 125 | 38% helix, 6% strand | Q8NP09 |
| F, f | Cytochrome C oxidase polypeptide 4 (EC 7.1.1.9) | protein | 143 | 62% helix, 3% strand | Q8NNK3 |
| G, g | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 325 | 33% helix, 21% strand | Q8NNK2 |
| D, d | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 573 | 65% helix, 1% strand | Q79VD7 |
| A, a | Cytochrome BC1 complex rieske iron-sulfur subunit | protein | 400 | 33% helix, 19% strand | Q79VE8 |
| L, l | Uncharacterized protein CGL2664/CG2949 | protein | 153 | 2% helix, 35% strand | Q8NMB4 |
| B, b | Cytochrome BC1 complex cytochrome B subunit (EC 7.1.1.8) | protein | 534 | 61% helix, 7% strand | Q79VE9 |
| C, c | Cytochrome BC1 complex cytochrome C subunit (EC 7.1.1.8) | protein | 232 | 40% helix, 3% strand | Q8NNK5 |
| y | Co-purified unknown transmembrane helices built as polyala (ascd) | protein | 91 | 49% helix, 0% strand | — |
| h | Uncharacterized membrane protein CGL2017/CG2211 | protein | 126 | 42% helix, 3% strand | Q8NP09 |
| X | Co-purified unknown peptide built as polyala (asce) | protein | 21 | 0% helix, 5% strand | — |
| x | Co-purified unknown peptide built as polyala (asce) | protein | 22 | 0% helix, 0% strand | — |
| V, v | Actinobacterial supercomplex, subunit C (ascc) | protein | 54 | 0% helix, 2% strand | Q8NS61 |
| K, k | Hypothetical membrane protein | protein | 63 | 73% helix, 5% strand | Q8NSJ8 |
Ligands and binding sites
- TRD · Tridecane · ligand · 18 copies · chains E, F, Y, D, A, b, a, H, B, e, f, y, d, h
- 7PH · (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate · ligand · 16 copies · chains E, F, D, H, B, C, G, Y, K, e, f, d, h, b, c, g, k, y
- CDL · Cardiolipin · ligand · 14 copies · chains E, A, B, C, F, D, V, b, e, a, c, f, d, v
- MQ9 · Menaquinone-9 · ligand · 6 copies · chains A, B, a, b
- 9XX · (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate · ligand · 4 copies · chains H, D, L, B, X, h, d, l, b, x
- HAS · Heme-as · ligand · 4 copies · chains G, D, g, d
- 9YF · (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 · ligand · 4 copies · chains H, D, L, B, C, A, a, b, h, d, l, c
- PLM · Palmitic acid · ligand · 4 copies · chains D, L, d, l, B, X, b, x
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, b
- HEC · Heme C · ligand · 4 copies · chains G, L, C, A, g, l, c, a
- TWT · Docosane · ligand · 2 copies · chains H, B, h, b
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, a
- CU · Copper (II) ion · metal · 6 copies · chains G, D, g, d
- MG · Magnesium ion · metal · 2 copies · chains G, D, g, d
- CA · Calcium ion · metal · 2 copies · chains D, d
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.90 | 0.91 | 113 | MG, HAS |
| 2 | 1076 | 0.90 | 0.91 | 108 | MG, HAS |
| 3 | 1023 | 0.87 | 0.87 | 76 | CDL |
| 4 | 946 | 0.86 | 0.87 | 79 | CDL |
| 5 | 666 | 0.86 | 0.90 | 77 | HEM |
Interfaces
87 interfaces between chains.
- A–B · 4881 Ų buried · 47 hydrogen bonds · protein-protein
- a–b · 4863 Ų buried · 45 hydrogen bonds · protein-protein
- g–d · 4758 Ų buried · 48 hydrogen bonds · protein-protein
- G–D · 4729 Ų buried · 50 hydrogen bonds · protein-protein
- A–a · 3330 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor, 4 disulfide (heme c attachment, disulfide).
Compared structures
- 7Q21 · III2-IV2 respiratory supercomplex from Corynebacterium glutamicum · the same entry in another collection · chain y against y, 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
- Every structure of UniProt Q9AEL8
- Every structure of UniProt Q8NP09
- Every structure of UniProt Q8NNK3
- Every structure of UniProt Q8NNK2
- Every structure of UniProt Q79VD7
- Every structure of UniProt Q79VE8
- Every structure of UniProt Q8NMB4
- Every structure of UniProt Q79VE9
- Every structure of UniProt Q8NNK5
- Every structure of UniProt Q8NS61
- Every structure of UniProt Q8NSJ8
- Elsewhere: RCSB PDB 7Q21 · PDBe 7Q21 · UniProt Q9AEL8 · UniProt Q8NP09 · UniProt Q8NNK3 · UniProt Q8NNK2 · UniProt Q79VD7 · UniProt Q79VE8 · UniProt Q8NMB4 · UniProt Q79VE9 · UniProt Q8NNK5 · UniProt Q8NS61 · UniProt Q8NSJ8
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