Research workbench
The structural basis for DNA protection by E. COLI dps protein
Analyse The structural basis for DNA protection by E. COLI dps protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F33
- Type
- protein
- Length
- 1,878 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA protection during starvation protein
- UniProt
- P0ABT2
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, J, K, L | DNA protection during starvation protein | protein | 156 | 72% helix, 1% strand | P0ABT2 |
| F, I | DNA protection during starvation protein | protein | 159 | 70% helix, 1% strand | P0ABT2 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 12 copies · chains A, D, E, B, C, F, G, I, K, H, L, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.75 | 0.98 | 20 | empty |
| 2 | 69 | 0.74 | 0.98 | 20 | empty |
| 3 | 66 | 0.74 | 0.98 | 20 | empty |
| 4 | 69 | 0.74 | 0.98 | 20 | empty |
| 5 | 583 | 0.63 | 0.74 | 62 | empty |
Interfaces
21 interfaces between chains.
- I–J · 1604 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1598 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1592 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 768 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1F33 · The structural basis for DNA protection by E. COLI dps protein · the same entry in another collection · chain L against L, 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 P0ABT2
- Elsewhere: RCSB PDB 1F33 · PDBe 1F33 · UniProt P0ABT2
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