MolNFT v1 · #176194 · protein
Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism
7DEG · Cytochrome C oxidase subunit I: “Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism”. Electron microscopy, 7 ligands (PGV, HAS, HEM), 15 pockets (best druggability 0.89). MolNFT…
- PDB
- 7DEG
- Type
- protein
- Length
- 1,520 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit I; Cytochrome oxidase subunit iia; Cytochrome oxidase…
- UniProt
- O67937, G5DGC8
- Ligands
- PGV, HAS, HEM, DLX, 3PE, CUA, CU
- Pockets
- 15 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 51% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytochrome C oxidase subunit I | protein | 581 | 59% helix, 0% strand | O67937 |
| C, F | Cytochrome oxidase subunit iia | protein | 32 | 59% helix, 0% strand | — |
| B, E | Cytochrome oxidase subunit II | protein | 147 | 16% helix, 31% strand | G5DGC8 |
Ligands and binding sites
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 6 copies · chains A, D, C, F
- HAS · Heme-as · ligand · 2 copies · chains A, C, D, F
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, D
- DLX · 2-[(2~{E},6~{E},10~{Z},14~{Z},18~{Z},23~{R})-3,7,11,15, 19,23,27-heptamethyloctacosa-2,6,10,14,18-pentaenyl]naphthalene-1,4-dione · ligand · 2 copies · chains A, C, D, F
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, C, D, F
- CUA · Dinuclear copper ion · ligand · 2 copies · chains B, E
- CU · Copper (II) ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.89 | 0.93 | 92 | HAS, HEM |
| 2 | 733 | 0.89 | 0.93 | 92 | HAS, HEM |
| 3 | 190 | 0.68 | 0.85 | 27 | DLX |
| 4 | 161 | 0.67 | 0.86 | 27 | DLX |
| 5 | 321 | 0.64 | 0.80 | 29 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2705 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2702 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1189 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1183 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1113 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent, 2 cofactor (covalent ligand, heme attachment).
Compared structures
- 7DEG · Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its… · the same entry in another collection · chain A against A, 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 O67937
- Every structure of UniProt G5DGC8
- Elsewhere: RCSB PDB 7DEG · PDBe 7DEG · UniProt O67937 · UniProt G5DGC8
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