Research workbench
Crystal structure of chlorite dismutase from magnetospirillum sp. in complex with azide
Analyse Crystal structure of chlorite dismutase from magnetospirillum sp. in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A12
- Type
- protein
- Length
- 1,210 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- Ligands
- HEM, AZI
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Chlorite dismutase (EC 1.13.11.49) | protein | 242 | 41% helix, 28% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A, B, C, D, E
- AZI · Azide ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 8 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.79 | 0.84 | 68 | HEM, AZI, GOL |
| 2 | 565 | 0.79 | 0.85 | 56 | HEM, AZI, GOL |
| 3 | 554 | 0.78 | 0.85 | 61 | HEM, AZI, GOL |
| 4 | 577 | 0.78 | 0.84 | 59 | HEM, AZI, GOL |
| 5 | 597 | 0.78 | 0.84 | 54 | HEM, AZI, GOL |
Interfaces
5 interfaces between chains.
- B–C · 1454 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1441 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1441 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 1424 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1415 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5A12 · Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with azide · 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
- Elsewhere: RCSB PDB 5A12 · PDBe 5A12
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