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The structure of biphenyl-2,3-diol 1,2-dioxygenase iii-related protein from salmonella typhimurium
Analyse The structure of biphenyl-2,3-diol 1,2-dioxygenase iii-related protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HUH
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium
- Molecule
- Virulence protein STM3117
- UniProt
- Q8ZM36
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 16% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Virulence protein STM3117 | protein | 124 | 16% helix, 48% strand | Q8ZM36 |
| B, C | Virulence protein STM3117 | protein | 119 | 17% helix, 45% strand | Q8ZM36 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.73 | 0.98 | 27 | empty |
| 2 | 65 | 0.73 | 0.98 | 31 | empty |
| 3 | 71 | 0.65 | 0.93 | 19 | empty |
| 4 | 83 | 0.61 | 0.90 | 17 | empty |
| 5 | 228 | 0.58 | 0.80 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2409 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2383 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 158 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HUH · The structure of biphenyl-2,3-diol 1,2-dioxygenase III-related protein from salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZM36 · AlphaFold monomer V2.0 prediction for virulence protein STM3117 (Q8ZM36) · 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 Q8ZM36
- Elsewhere: RCSB PDB 3HUH · PDBe 3HUH · UniProt Q8ZM36
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