Research workbench
Structure of the effector protein TSE1 from pseudomonas aeruginosa, selenomethionine variant
Analyse Structure of the effector protein TSE1 from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FGD
- Type
- protein
- Length
- 588 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TSE1
- UniProt
- Q9I2Q1
- Ligands
- SCN, CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TSE1 | protein | 148 | 32% helix, 20% strand | Q9I2Q1 |
| B | TSE1 | protein | 146 | 39% helix, 25% strand | Q9I2Q1 |
| C | TSE1 | protein | 147 | 37% helix, 20% strand | Q9I2Q1 |
| D | TSE1 | protein | 147 | 37% helix, 24% strand | Q9I2Q1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.69 | 0.75 | 99 | CL |
| 2 | 120 | 0.49 | 0.80 | 27 | SCN |
| 3 | 109 | 0.47 | 0.80 | 27 | empty |
| 4 | 102 | 0.45 | 0.79 | 26 | empty |
| 5 | 70 | 0.30 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–C · 714 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 706 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 396 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 4FGD · Structure of the effector protein Tse1 from Pseudomonas aeruginosa, selenomethionine… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9I2Q1 · AlphaFold monomer V2.0 prediction for peptidoglycan amidase TSE1 (Q9I2Q1) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9I2Q1
- Elsewhere: RCSB PDB 4FGD · PDBe 4FGD · UniProt Q9I2Q1
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