Research workbench
Crystal structure of protein STHE_2403 from sphaerobacter thermophilus
Analyse Crystal structure of protein STHE_2403 from sphaerobacter thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TGN
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- D1C7H4
- Ligands
- CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uncharacterized protein | protein | 109 | 25% helix, 47% strand | D1C7H4 |
| B | Uncharacterized protein | protein | 108 | 25% helix, 48% strand | D1C7H4 |
| C | Uncharacterized protein | protein | 107 | 26% helix, 47% strand | D1C7H4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.80 | 0.95 | 31 | GOL, CL |
| 2 | 760 | 0.78 | 0.82 | 86 | GOL, CL |
| 3 | 134 | 0.47 | 0.78 | 27 | GOL |
| 4 | 106 | 0.41 | 0.76 | 27 | empty |
| 5 | 110 | 0.36 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 799 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 776 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 627 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 626 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5TGN · Crystal structure of protein Sthe_2403 from Sphaerobacter thermophilus · 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 D1C7H4
- Elsewhere: RCSB PDB 5TGN · PDBe 5TGN · UniProt D1C7H4
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