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Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W146Y R173Q
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
- 4M09
- 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, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chlorite dismutase (EC 1.13.11.49) | protein | 238 | 39% helix, 27% strand | B3U4H7 |
| C, D | Chlorite dismutase (EC 1.13.11.49) | protein | 236 | 39% helix, 28% strand | B3U4H7 |
| E | Chlorite dismutase (EC 1.13.11.49) | protein | 237 | 38% helix, 29% strand | B3U4H7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, D, C, E
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, D, C, E
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, D, C, E
- IMD · Imidazole · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.80 | 0.84 | 51 | HEM, EDO |
| 2 | 657 | 0.80 | 0.85 | 53 | HEM, IMD |
| 3 | 677 | 0.80 | 0.84 | 50 | HEM, IMD |
| 4 | 640 | 0.80 | 0.84 | 47 | HEM |
| 5 | 712 | 0.79 | 0.83 | 56 | HEM |
Interfaces
5 interfaces between chains.
- B–D · 1603 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1593 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1575 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1552 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4M09 · Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W146Y… · the same entry in another collection · chain B against B, 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 4M09 · PDBe 4M09 · UniProt B3U4H7
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