Research workbench
Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145F in complex with cyanide
Analyse Crystal structure of mutant chlorite dismutase from candidatus nitrospira… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M06
- Type
- protein
- Length
- 1,185 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- UniProt
- B3U4H7
- Ligands
- HEM, CYN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Chlorite dismutase (EC 1.13.11.49) | protein | 235 | 40% helix, 28% strand | B3U4H7 |
| B, E | Chlorite dismutase (EC 1.13.11.49) | protein | 239 | 40% helix, 28% strand | B3U4H7 |
| C | Chlorite dismutase (EC 1.13.11.49) | protein | 237 | 41% helix, 27% strand | B3U4H7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, D, C, E
- CYN · Cyanide ion · ion · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D, E
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.81 | 0.86 | 48 | HEM, CYN |
| 2 | 667 | 0.81 | 0.85 | 55 | HEM, CYN |
| 3 | 613 | 0.80 | 0.85 | 50 | HEM, CYN |
| 4 | 616 | 0.80 | 0.85 | 53 | HEM, CYN |
| 5 | 638 | 0.80 | 0.85 | 54 | HEM, CYN, EDO |
Interfaces
5 interfaces between chains.
- A–E · 1636 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1615 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1611 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1604 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1513 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4M06 · Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F… · 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 B3U4H7
- Elsewhere: RCSB PDB 4M06 · PDBe 4M06 · UniProt B3U4H7
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