MolNFT v1 · #191383 · protein
Cryo-EM structure of saccharomyces cerevisiae cytochrome C oxidase (complex IV) extracted in lipid nanodiscs
8DH6 · Cytochrome C oxidase subunit 1: “Cryo-EM structure of saccharomyces cerevisiae cytochrome C oxidase (complex IV) extracted in lipid nanodiscs”. Electron microscopy, 6 ligands (PEF, HEA, CU), 20 pockets (best druggability 0.91).…
- PDB
- 8DH6
- Type
- protein
- Length
- 1,560 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 7.1.1.9
- UniProt
- P00401, P00410, P00420, P04037, P00424, P00427, P10174, P04039, P07255
- Ligands
- PEF, HEA, CU, CA, MG, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 9 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 534 | 69% helix, 1% strand | P00401 |
| b | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 236 | 34% helix, 25% strand | P00410 |
| c | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 269 | 74% helix, 0% strand | P00420 |
| d | Cytochrome C oxidase subunit 4, mitochondrial | protein | 121 | 16% helix, 17% strand | P04037 |
| e | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 133 | 59% helix, 0% strand | P00424 |
| f | Cytochrome C oxidase subunit 6, mitochondrial | protein | 102 | 72% helix, 1% strand | P00427 |
| g | Cytochrome C oxidase subunit 7, mitochondrial | protein | 59 | 64% helix, 0% strand | P10174 |
| h | Cytochrome C oxidase subunit 8, mitochondrial | protein | 51 | 49% helix, 0% strand | P04039 |
| i | Cytochrome C oxidase subunit 9, mitochondrial | protein | 55 | 85% helix, 2% strand | P07255 |
Ligands and binding sites
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 10 copies · chains a, c, e, h, b, i, d, g
- HEA · Heme-A · ligand · 2 copies · chains a, b
- CU · Copper (II) ion · metal · 2 copies · chains a, b
- CA · Calcium ion · metal · chains a
- MG · Magnesium ion · metal · chains a, b
- ZN · Zinc ion · metal · chains 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.91 | 0.93 | 103 | HEA |
| 2 | 855 | 0.84 | 0.86 | 79 | PEF |
| 3 | 194 | 0.79 | 0.93 | 26 | empty |
| 4 | 390 | 0.78 | 0.87 | 51 | empty |
| 5 | 579 | 0.71 | 0.79 | 64 | PEF |
Interfaces
22 interfaces between chains.
- a–b · 3647 Ų buried · 27 hydrogen bonds · protein-protein
- a–c · 2548 Ų buried · 15 hydrogen bonds · protein-protein
- a–h · 1848 Ų buried · 10 hydrogen bonds · protein-protein
- a–e · 1703 Ų buried · 22 hydrogen bonds · protein-protein
- c–g · 1448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 8DH6 · Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted… · the same entry in another collection · chain i against i, TM-score 1.00
- P00410 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (P00410) · a predicted model of the same protein · chain b against A, TM-score 0.99
- P00427 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 6, mitochondrial… · a predicted model of the same protein · chain f against A, TM-score 0.98
- P00420 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 3 (P00420) · a predicted model of the same protein · chain c against A, TM-score 0.97
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 P00401
- Every structure of UniProt P00410
- Every structure of UniProt P00420
- Every structure of UniProt P04037
- Every structure of UniProt P00424
- Every structure of UniProt P00427
- Every structure of UniProt P10174
- Every structure of UniProt P04039
- Every structure of UniProt P07255
- Elsewhere: RCSB PDB 8DH6 · PDBe 8DH6 · UniProt P00401 · UniProt P00410 · UniProt P00420 · UniProt P04037 · UniProt P00424 · UniProt P00427 · UniProt P10174 · UniProt P04039 · UniProt P07255
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