Research workbench
The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding
Analyse The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O9R
- Type
- protein
- Length
- 967 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- AGROBACTERIUM TUMEFACIENS
- Molecule
- Agrobacterium tumefaciens dps
- UniProt
- Q8UCK6
- Ligands
- FE
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.45 · 3 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Agrobacterium tumefaciens dps | protein | 162 | 72% helix, 1% strand | Q8UCK6 |
| C | Agrobacterium tumefaciens dps | protein | 159 | 74% helix, 1% strand | Q8UCK6 |
| D | Agrobacterium tumefaciens dps | protein | 160 | 73% helix, 1% strand | Q8UCK6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains B, D, A, C, E
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.66 | 0.83 | 23 | empty |
| 2 | 143 | 0.65 | 0.87 | 33 | empty |
| 3 | 56 | 0.54 | 0.89 | 19 | empty |
| 4 | 188 | 0.52 | 0.78 | 32 | empty |
| 5 | 91 | 0.39 | 0.77 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1551 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1532 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 825 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 821 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 806 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1O9R · The X-ray crystal structure of agrobacterium tumefaciens dps, a member of the family that… · the same entry in another collection · chain F against F, TM-score 1.00
- Q8UCK6 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (Q8UCK6) · a predicted model of the same protein · chain C 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 Q8UCK6
- Elsewhere: RCSB PDB 1O9R · PDBe 1O9R · UniProt Q8UCK6
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