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Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 in complex with isothiocyanate
Analyse Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K90
- Type
- protein
- Length
- 698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- UniProt
- B8HNS6
- Ligands
- IS8, HEM, MG, SO4
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chlorite dismutase | protein | 174 | 31% helix, 36% strand | B8HNS6 |
| B, D | Chlorite dismutase | protein | 175 | 31% helix, 35% strand | B8HNS6 |
| C | Chlorite dismutase | protein | 174 | 31% helix, 36% strand | B8HNS6 |
Ligands and binding sites
- IS8 · isothiocyanate · ligand · 4 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.86 | 0.87 | 105 | IS8, HEM, GOL |
| 2 | 527 | 0.80 | 0.86 | 57 | GOL, HEM, IS8 |
| 3 | 522 | 0.80 | 0.86 | 58 | IS8, HEM |
| 4 | 76 | 0.39 | 0.78 | 13 | GOL |
| 5 | 74 | 0.39 | 0.78 | 14 | GOL |
Interfaces
2 interfaces between chains.
- C–D · 949 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5K90 · Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 in complex… · 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 5K90 · PDBe 5K90 · UniProt B8HNS6
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