MolNFT v1 · #124230 · protein
Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 in complex with isothiocyanate
5K90: “Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 in complex with isothiocyanate”. X-ray diffraction, 4 ligands (IS8, HEM, MG), 9 pockets (best druggability 0.86). MolNFT v1 #124230 on GenesisL1: 3D…
- 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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