MolNFT v1 · #99328 · protein
Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145V
4M08: “Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145V”. X-ray diffraction, 2 ligands (HEM, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #99328 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4M08
- Type
- protein
- Length
- 1,190 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 0.82
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 238 | 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 · 22 copies · chains A, E, C, B, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B, D, E
- IMD · Imidazole · additive · 5 copies · chains A, B, C, D, E
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 | 652 | 0.82 | 0.86 | 53 | HEM, SO4, IMD |
| 2 | 746 | 0.82 | 0.85 | 63 | HEM, IMD, SO4, EDO |
| 3 | 807 | 0.82 | 0.84 | 70 | SO4, HEM, IMD |
| 4 | 787 | 0.81 | 0.84 | 61 | HEM, SO4, IMD |
| 5 | 765 | 0.81 | 0.84 | 62 | SO4, HEM, IMD |
Interfaces
5 interfaces between chains.
- B–D · 1578 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1562 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1555 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1545 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1516 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4M08 · Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145V · 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 4M08 · PDBe 4M08 · UniProt B3U4H7
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