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Joint neutron/X-ray structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425
Analyse Joint neutron/X-ray structure of dimeric chlorite dismutase from Cyanothece sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NKU
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction, neutron diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2,2.35
- Source
- Cyanothece sp. (strain PCC 7425 / ATCC 29141)
- Molecule
- Chlorite Dismutase
- UniProt
- B8HNS6
- Ligands
- HEM, OH, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction, neutron diffraction · resolution 2,2.35 · 2 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chlorite Dismutase | protein | 179 | 29% helix, 36% strand | B8HNS6 |
| B | Chlorite Dismutase | protein | 178 | 31% helix, 36% strand | B8HNS6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OH · Hydroxide ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.81 | 0.87 | 52 | HEM, OH |
| 2 | 547 | 0.80 | 0.86 | 57 | HEM, OH |
| 3 | 77 | 0.45 | 0.81 | 17 | empty |
| 4 | 79 | 0.40 | 0.78 | 10 | GOL |
| 5 | 63 | 0.35 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 989 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5NKU · Joint NEUTRON/X-ray structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 · 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 B8HNS6
- Elsewhere: RCSB PDB 5NKU · PDBe 5NKU · UniProt B8HNS6
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