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The crystal structure of chlorite dismutase: a detox enzyme producing molecular oxygen
Analyse The crystal structure of chlorite dismutase: a detox enzyme producing molecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VXH
- Type
- protein
- Length
- 1,375 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- UniProt
- Q673K5
- Ligands
- HEM, SCN, CO3
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chlorite dismutase (EC 1.13.11.49) | protein | 228 | 39% helix, 26% strand | Q673K5 |
| B | Chlorite dismutase (EC 1.13.11.49) | protein | 230 | 39% helix, 26% strand | Q673K5 |
| C | Chlorite dismutase (EC 1.13.11.49) | protein | 228 | 40% helix, 26% strand | Q673K5 |
| D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 230 | 40% helix, 26% strand | Q673K5 |
| F | Chlorite dismutase (EC 1.13.11.49) | protein | 229 | 40% helix, 26% strand | Q673K5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- SCN · Thiocyanate ion · ion · 6 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 5 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.77 | 0.79 | 95 | HEM, SCN, CO3 |
| 2 | 943 | 0.77 | 0.79 | 76 | HEM, SCN, CO3 |
| 3 | 877 | 0.76 | 0.79 | 76 | HEM, SCN |
| 4 | 937 | 0.75 | 0.78 | 76 | HEM, SCN, CO3 |
| 5 | 768 | 0.75 | 0.79 | 71 | HEM, SCN, CO3 |
Interfaces
6 interfaces between chains.
- A–F · 1372 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1370 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1368 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1366 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1364 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2VXH · The crystal structure of chlorite dismutase: a detox enzyme producing molecular oxygen · 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 Q673K5
- Elsewhere: RCSB PDB 2VXH · PDBe 2VXH · UniProt Q673K5
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