Research workbench
Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes
Analyse Protein-DNA recognition and DNA deformation revealed in crystal structures of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O3Q
- Type
- protein + DNA
- Length
- 226 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'; 5'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3' | dna | 11 | — | — |
| C | 5'- D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*T)-3' | dna | 15 | — | — |
| A | Catabolite gene activator protein | protein | 200 | 41% helix, 30% strand | P0ACJ8 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.72 | 0.79 | 69 | CMP |
| 2 | 112 | 0.35 | 0.73 | 15 | CMP |
| 3 | 57 | 0.31 | 0.77 | 12 | empty |
| 4 | 52 | 0.31 | 0.77 | 11 | empty |
| 5 | 56 | 0.28 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 479 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- C–A · 392 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–A · 350 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1O3Q · Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P0ACJ8 · AlphaFold monomer V2.0 prediction for camp-activated global transcriptional regulator crp… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P0ACJ8
- Elsewhere: RCSB PDB 1O3Q · PDBe 1O3Q · UniProt P0ACJ8
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