Research workbench
M.ACETIVORANS protoglobin in complex with cyanide
Analyse M.ACETIVORANS protoglobin in complex with cyanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZJN
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoglobin
- UniProt
- Q8TLY9
- Ligands
- HEM, CYN, PO4
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protoglobin | protein | 190 | 66% helix, 2% strand | Q8TLY9 |
| B | Protoglobin | protein | 191 | 65% helix, 2% strand | Q8TLY9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.86 | 0.96 | 39 | HEM, CYN |
| 2 | 300 | 0.86 | 0.96 | 40 | HEM, CYN |
| 3 | 55 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1930 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3ZJN · M.acetivorans protoglobin in complex with cyanide · 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 Q8TLY9
- Elsewhere: RCSB PDB 3ZJN · PDBe 3ZJN · UniProt Q8TLY9
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