Research workbench
Crystal structure of chlorite dismutase from magnetospirillum sp. in complex with thiocyanate
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
- 5A13
- Type
- protein
- Length
- 2,426 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- EC
- 1.13.11.49
- Ligands
- HEM, SCN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, H, I, J | Chlorite dismutase (EC 1.13.11.49) | protein | 242 | 40% helix, 28% strand | — |
| B, G | Chlorite dismutase (EC 1.13.11.49) | protein | 245 | 40% helix, 27% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SCN · Thiocyanate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- GOL · Glycerol · additive · 14 copies · chains A, B, C, E, D, F, G, H, J, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.80 | 0.85 | 52 | HEM, SCN, GOL |
| 2 | 680 | 0.79 | 0.84 | 79 | HEM, SCN, GOL |
| 3 | 563 | 0.79 | 0.85 | 56 | HEM, SCN, GOL |
| 4 | 630 | 0.79 | 0.84 | 60 | HEM, SCN, GOL |
| 5 | 556 | 0.78 | 0.84 | 59 | HEM, SCN, GOL |
Interfaces
12 interfaces between chains.
- F–J · 1447 Ų buried · 27 hydrogen bonds · protein-protein
- F–I · 1444 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1444 Ų buried · 29 hydrogen bonds · protein-protein
- H–J · 1443 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1443 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5A13 · Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with… · 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
- Elsewhere: RCSB PDB 5A13 · PDBe 5A13
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