MolNFT v1 · #20935 · protein + DNA
Catabolite gene activator protein (cap) MUTANT/DNA complex + adenosine-3',5'-cyclic-monophosphate
1RUO · DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'): “Catabolite gene activator protein (cap) MUTANT/DNA complex + adenosine-3',5'-cyclic-monophosphate”. X-ray diffraction, 1 ligand (CMP), 5 pockets (best druggability 0.79).…
- PDB
- 1RUO
- Type
- protein + DNA
- Length
- 461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'); DNA (5'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3') | dna | 14 | — | — |
| D, F | DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3') | dna | 17 | — | — |
| A | Protein (catabolite gene activator protein (cap)) | protein | 198 | 37% helix, 21% strand | P0ACJ8 |
| B | Protein (catabolite gene activator protein (cap)) | protein | 201 | 37% helix, 22% strand | P0ACJ8 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.79 | 0.81 | 93 | CMP |
| 2 | 529 | 0.77 | 0.85 | 58 | CMP |
| 3 | 747 | 0.69 | 0.77 | 49 | empty |
| 4 | 410 | 0.59 | 0.76 | 45 | empty |
| 5 | 55 | 0.26 | 0.74 | 11 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1677 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 626 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- D–E · 619 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- F–A · 412 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 404 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1RUO · Catabolite gene activator protein (cap) MUTANT/DNA complex +… · 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 0.97
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 1RUO · PDBe 1RUO · UniProt P0ACJ8
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