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Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 (pH 8.5)
Analyse Crystal structure of dimeric chlorite dismutase from cyanothece sp. PCC7425 (pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K8Z
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- UniProt
- B8HNS6
- Ligands
- HEM, OH
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chlorite dismutase | protein | 181 | 30% helix, 34% strand | B8HNS6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OH · Hydroxide ion · ion · 4 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, 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 | 1085 | 0.85 | 0.86 | 103 | HEM, OH |
| 2 | 528 | 0.81 | 0.87 | 56 | HEM, OH |
| 3 | 556 | 0.80 | 0.86 | 60 | HEM, OH |
| 4 | 86 | 0.45 | 0.80 | 14 | MPD |
| 5 | 81 | 0.44 | 0.80 | 15 | MPD |
Interfaces
2 interfaces between chains.
- A–B · 974 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 955 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5K8Z · Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 8.5) · 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 5K8Z · PDBe 5K8Z · UniProt B8HNS6
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