MolNFT v1 · #161638 · protein
Structure of the azide-inhibited form of cytochrome C peroxidase from obligate human pathogenic bacterium neisseria gonorrhoeae
6QKN · Cytochrome-C peroxidase: “Structure of the azide-inhibited form of cytochrome C peroxidase from obligate human pathogenic bacterium…”. X-ray diffraction, 3 ligands (HEC, CA, AZI), 6 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 6QKN
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome-C peroxidase
- EC
- 1.11.1.5
- UniProt
- A0A1D3HIT0
- Ligands
- HEC, CA, AZI
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome-C peroxidase (EC 1.11.1.5) | protein | 329 | 46% helix, 4% strand | A0A1D3HIT0 |
| B | Cytochrome-C peroxidase (EC 1.11.1.5) | protein | 323 | 45% helix, 4% strand | A0A1D3HIT0 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.87 | 0.92 | 74 | HEC, AZI |
| 2 | 562 | 0.87 | 0.92 | 75 | HEC, AZI |
| 3 | 525 | 0.84 | 0.90 | 72 | empty |
| 4 | 55 | 0.45 | 0.84 | 17 | empty |
| 5 | 59 | 0.39 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1687 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 6QKN · Structure of the azide-inhibited form of cytochrome c peroxidase from obligate human… · 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 A0A1D3HIT0
- Elsewhere: RCSB PDB 6QKN · PDBe 6QKN · UniProt A0A1D3HIT0
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