Research workbench
The crystal structure of SeMet-CT
Analyse The crystal structure of SeMet-CT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EGF
- Type
- protein
- Length
- 1,771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.29
- Source
- Penicillium aethiopicum
- Molecule
- TqaA
- UniProt
- F1CWE4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.29 · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | TqaA | protein | 442 | 33% helix, 24% strand | F1CWE4 |
| B | TqaA | protein | 443 | 33% helix, 24% strand | F1CWE4 |
| C | TqaA | protein | 444 | 34% helix, 23% strand | F1CWE4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 35 copies · chains A, B, C, D
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains A, D, B, C
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 | 767 | 0.85 | 0.87 | 57 | EDO, C8E |
| 2 | 708 | 0.84 | 0.87 | 59 | C8E, EDO |
| 3 | 443 | 0.74 | 0.83 | 44 | EDO |
| 4 | 636 | 0.73 | 0.80 | 60 | EDO |
| 5 | 372 | 0.72 | 0.83 | 45 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 1160 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1040 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 924 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5EGF · The crystal structure of semet-ct · 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
- Every structure of UniProt F1CWE4
- Elsewhere: RCSB PDB 5EGF · PDBe 5EGF · UniProt F1CWE4
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