Research workbench
Structure of chlorite dismutase from candidatus nitrospira defluvii R173A mutant
Analyse Structure of chlorite dismutase from candidatus nitrospira defluvii R173A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NN3
- Type
- protein
- Length
- 1,190 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- UniProt
- B3U4H7
- Ligands
- HEM, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 238 | 44% helix, 28% strand | B3U4H7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 20 copies · chains A, E, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.79 | 0.81 | 80 | SO4, HEM |
| 2 | 822 | 0.79 | 0.81 | 60 | HEM, SO4 |
| 3 | 914 | 0.79 | 0.81 | 81 | HEM, SO4 |
| 4 | 777 | 0.78 | 0.82 | 58 | HEM, SO4 |
| 5 | 795 | 0.78 | 0.81 | 66 | HEM, SO4 |
Interfaces
5 interfaces between chains.
- A–C · 1540 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1517 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1482 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1479 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1472 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3NN3 · Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173A mutant · 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 B3U4H7
- Elsewhere: RCSB PDB 3NN3 · PDBe 3NN3 · UniProt B3U4H7
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