Research workbench
Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 a resolution
Analyse Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NKZ
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable integral membrane cytochrome D ubiquinol oxidase (subunit II) cydb (cytochrome…
- UniProt
- O06139, L7N662
- Ligands
- HEB, MQ9, HDD, OXY
- Pockets
- 8 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable integral membrane cytochrome D ubiquinol oxidase (subunit II) cydb (cytochrome bd-I oxidase subunit II) | protein | 337 | 74% helix, 4% strand | O06139 |
| A | Probable integral membrane cytochrome D ubiquinol oxidase (subunit I) cyda (cytochrome bd-I oxidase subunit I) | protein | 455 | 73% helix, 5% strand | L7N662 |
Ligands and binding sites
- HEB · Heme B/C · ligand · 2 copies · chains A
- MQ9 · Menaquinone-9 · ligand · chains A
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · chains B, A
- OXY · Oxygen molecule · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.85 | 0.89 | 61 | OXY, MQ9, HDD, HEB |
| 2 | 395 | 0.78 | 0.87 | 44 | HEB |
| 3 | 549 | 0.73 | 0.81 | 56 | empty |
| 4 | 266 | 0.56 | 0.77 | 39 | empty |
| 5 | 185 | 0.53 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- B–A · 3049 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NKZ · Cryo-EM structure of the cytochrome bd oxidase from M. tuberculosis at 2.5 A resolution · the same entry in another collection · chain B against B, 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 O06139
- Every structure of UniProt L7N662
- Elsewhere: RCSB PDB 7NKZ · PDBe 7NKZ · UniProt O06139 · UniProt L7N662
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