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The structure of CBB3 cytochrome oxidase
Analyse The structure of CBB3 cytochrome oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MK7
- Type
- protein
- Length
- 3,979 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase, CBB3-type, subunit N; Cytochrome C oxidase, CBB3-type, subunit O…
- Ligands
- HEC, HEM, PEO, FC6, CA, CU, PO4
- Pockets
- 20 · best druggability 0.92
Structure
x-ray diffraction · 6 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase, CBB3-type, subunit N | protein | 466 | 76% helix, 3% strand | — |
| B, E, H, L | Cytochrome C oxidase, CBB3-type, subunit O | protein | 197 | 49% helix, 2% strand | — |
| C, F, I, M | Cytochrome C oxidase, CBB3-type, subunit P | protein | 303 | 54% helix, 4% strand | — |
| D | Cytochrome C oxidase, CBB3-type, subunit N | protein | 463 | 77% helix, 3% strand | — |
| G, K | Cytochrome C oxidase, CBB3-type, subunit N | protein | 465 | 76% helix, 3% strand | — |
| U, X, Y, Z | 30-mer peptide | protein | 30 | 77% helix, 0% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 12 copies · chains A, B, C, I, D, E, F, G, H, K, L, M
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, D, E, G, H, K, L
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, D, G, K
- FC6 · Hexacyanoferrate(3-) · ligand · 4 copies · chains C, M, F, I
- CA · Calcium ion · metal · 8 copies · chains A, B, D, E, G, H, K, L
- CU · Copper (II) ion · metal · 4 copies · chains A, D, G, K
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, F, G, I, K, M
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 | 849 | 0.92 | 0.95 | 136 | HEC |
| 2 | 715 | 0.90 | 0.93 | 105 | HEC |
| 3 | 811 | 0.89 | 0.92 | 114 | HEC, FC6 |
| 4 | 489 | 0.88 | 0.95 | 80 | HEC |
| 5 | 492 | 0.88 | 0.94 | 70 | HEM, CA, PEO |
Interfaces
29 interfaces between chains.
- A–B · 3782 Ų buried · 29 hydrogen bonds · protein-protein
- K–L · 3780 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 3769 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 3762 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 2594 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor (heme c attachment).
Compared structures
- 3MK7 · The structure of CBB3 cytochrome oxidase · 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
- Elsewhere: RCSB PDB 3MK7 · PDBe 3MK7
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