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Crystal structure of dimeric chlorite dismutase variant R127A (ccld R127A) from cyanothece sp. PCC7425 in complex with nitrite
Analyse Crystal structure of dimeric chlorite dismutase variant R127A (ccld R127A) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OUY
- Type
- protein
- Length
- 704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- UniProt
- B8HNS6
- Ligands
- HEM, NO2, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chlorite dismutase | protein | 176 | 31% helix, 36% strand | B8HNS6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NO2 · Nitrite ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.81 | 0.84 | 69 | GOL, PGE, HEM, NO2 |
| 2 | 583 | 0.81 | 0.86 | 58 | GOL, HEM, NO2 |
| 3 | 646 | 0.80 | 0.85 | 68 | PGE, HEM, NO2, GOL |
| 4 | 667 | 0.80 | 0.84 | 69 | PGE, HEM, NO2, GOL |
| 5 | 103 | 0.41 | 0.77 | 19 | PGE |
Interfaces
2 interfaces between chains.
- C–D · 1007 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7OUY · Crystal structure of dimeric chlorite dismutase variant R127A (CCld R127A) from… · 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 7OUY · PDBe 7OUY · UniProt B8HNS6
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