MolNFT v1 · #106657 · protein
Crystal structure of thiol dioxygenase from pseudomonas aeruginosa
4TLF · 3-mercaptopropionate dioxygenase: “Crystal structure of thiol dioxygenase from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (FE2), 12 pockets (best druggability 0.63). MolNFT v1 #106657 on GenesisL1: 3D structure, binding…
- PDB
- 4TLF
- Type
- protein
- Length
- 781 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
- 12 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 194 | 22% helix, 35% strand | Q9I0N5 |
| B | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 193 | 19% helix, 35% strand | Q9I0N5 |
| C | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 196 | 19% helix, 33% strand | Q9I0N5 |
| D | 3-mercaptopropionate dioxygenase (EC 1.13.11.-) | protein | 198 | 20% 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.63 | 0.88 | 29 | FE2 |
| 2 | 68 | 0.59 | 0.89 | 26 | empty |
| 3 | 298 | 0.54 | 0.75 | 34 | empty |
| 4 | 303 | 0.51 | 0.74 | 42 | empty |
| 5 | 136 | 0.42 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1311 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 351 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TLF · Crystal structure of Thiol dioxygenase from Pseudomonas aeruginosa · 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 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 Q9I0N5
- Elsewhere: RCSB PDB 4TLF · PDBe 4TLF · UniProt Q9I0N5
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