MolNFT v1 · #180090 · protein
Crystal structure of azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate
7KOV · Cysteine dioxygenase type I protein: “Crystal structure of azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate”. X-ray diffraction, 3 ligands (FE, SCN, CL), 4 pockets (best druggability 0.45).…
- PDB
- 7KOV
- Type
- protein
- Length
- 773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine dioxygenase type I protein
- UniProt
- C1DN94
- Ligands
- FE, SCN, CL
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cysteine dioxygenase type I protein | protein | 194 | 19% helix, 35% strand | C1DN94 |
| A, C, D | Cysteine dioxygenase type I protein | protein | 193 | 19% helix, 35% strand | C1DN94 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains B, A, C, D
- SCN · Thiocyanate ion · ion · 4 copies · chains B, A, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.45 | 0.78 | 21 | empty |
| 2 | 105 | 0.42 | 0.77 | 18 | empty |
| 3 | 130 | 0.37 | 0.73 | 21 | empty |
| 4 | 101 | 0.35 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1353 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1320 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 256 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KOV · Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in… · 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
- Every structure of UniProt C1DN94
- Elsewhere: RCSB PDB 7KOV · PDBe 7KOV · UniProt C1DN94
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