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Structure of chlorite dismutase from candidatus nitrospira defluvii in complex with cyanide
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
- 3NN2
- Type
- protein
- Length
- 1,194 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, CYN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chlorite dismutase (EC 1.13.11.49) | protein | 238 | 42% helix, 27% strand | B3U4H7 |
| B, C, D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 239 | 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 · 18 copies · chains A, C, E, B, D
- CYN · Cyanide ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 13 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.81 | 0.85 | 59 | PO4, HEM, CYN, GOL |
| 2 | 810 | 0.81 | 0.83 | 87 | PO4, HEM, CYN, GOL |
| 3 | 655 | 0.80 | 0.85 | 60 | HEM, PO4, CYN, GOL |
| 4 | 611 | 0.80 | 0.85 | 58 | HEM, PO4, CYN, GOL |
| 5 | 672 | 0.79 | 0.84 | 60 | HEM, PO4, CYN, GOL |
Interfaces
5 interfaces between chains.
- D–E · 1595 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1592 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1519 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1516 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1489 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3NN2 · Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with… · the same entry in another collection · chain D against D, 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 3NN2 · PDBe 3NN2 · UniProt B3U4H7
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