Research workbench
Crystal structure of artificial crosslinked thiol dioxygenase G95C variant from pseudomonas aeruginosa
Analyse Crystal structure of artificial crosslinked thiol dioxygenase G95C variant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WVZ
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-mercaptopropionate dioxygenase
- EC
- 1.13.11.-
- UniProt
- Q9I0N5
- Ligands
- FE2
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 195 | 21% helix, 34% strand | Q9I0N5 |
| C | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 201 | 22% helix, 33% strand | Q9I0N5 |
| D | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 203 | 19% helix, 33% strand | Q9I0N5 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.58 | 0.86 | 27 | FE2 |
| 2 | 105 | 0.57 | 0.85 | 27 | FE2 |
| 3 | 271 | 0.54 | 0.76 | 34 | empty |
| 4 | 137 | 0.48 | 0.78 | 22 | empty |
| 5 | 139 | 0.46 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1487 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4WVZ · Crystal structure of artificial crosslinked thiol dioxygenase G95C variant from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9I0N5 · AlphaFold monomer V2.0 prediction for 3-mercaptopropionate dioxygenase (Q9I0N5) · a predicted model of the same protein · chain B 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 Q9I0N5
- Elsewhere: RCSB PDB 4WVZ · PDBe 4WVZ · UniProt Q9I0N5
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