MolNFT v1 · #99326 · protein
Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145F in complex with cyanide
4M06: “Crystal structure of mutant chlorite dismutase from candidatus nitrospira defluvii W145F in complex with…”. X-ray diffraction, 2 ligands (HEM, CYN), 20 pockets (best druggability 0.81). MolNFT v1 #99326 on GenesisL1: 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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