Research workbench
Structure of chlorite dismutase from candidatus nitrospira defluvii in complex with imidazole
Analyse Structure of chlorite dismutase from candidatus nitrospira defluvii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NN1
- 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, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 238 | 43% helix, 27% strand | B3U4H7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 15 copies · chains A, C, B, D, E
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D, E
- IMD · Imidazole · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.81 | 0.85 | 62 | HEM, PO4, IMD, EDO |
| 2 | 695 | 0.81 | 0.85 | 61 | HEM, PO4, IMD, EDO |
| 3 | 650 | 0.81 | 0.85 | 58 | PO4, HEM, IMD, EDO |
| 4 | 793 | 0.80 | 0.83 | 85 | HEM, PO4, IMD, EDO |
| 5 | 647 | 0.79 | 0.83 | 56 | HEM, PO4, IMD, EDO |
Interfaces
5 interfaces between chains.
- A–C · 1596 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1583 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1544 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1540 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1490 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3NN1 · Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with… · 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 3NN1 · PDBe 3NN1 · UniProt B3U4H7
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