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Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145F
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
- 4M07
- Type
- protein
- Length
- 1,183 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Chlorite dismutase (EC 1.13.11.49) | protein | 235 | 38% helix, 28% strand | B3U4H7 |
| B, E | Chlorite dismutase (EC 1.13.11.49) | protein | 239 | 38% helix, 26% strand | B3U4H7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, D, C, E
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B, D, E
- GOL · Glycerol · additive · 6 copies · chains A, E, C, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.81 | 0.85 | 58 | HEM |
| 2 | 566 | 0.81 | 0.86 | 46 | HEM |
| 3 | 638 | 0.80 | 0.85 | 51 | HEM |
| 4 | 608 | 0.80 | 0.85 | 55 | HEM |
| 5 | 600 | 0.79 | 0.85 | 57 | HEM |
Interfaces
5 interfaces between chains.
- B–D · 1671 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1571 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1562 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1554 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1554 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4M07 · 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 4M07 · PDBe 4M07 · UniProt B3U4H7
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