Research workbench
Catabolite gene activator protein (CAP)/DNA complex + adenosine-3',5'-cyclic-monophosphate
Analyse Catabolite gene activator protein (CAP)/DNA complex +… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RUN
- Type
- protein + DNA
- Length
- 460 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
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% 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 | 201 | 36% helix, 27% strand | P0ACJ8 |
| B | Protein (catabolite gene activator protein (cap) ) | protein | 197 | 38% helix, 25% 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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.76 | 0.82 | 60 | CMP |
| 2 | 270 | 0.70 | 0.85 | 38 | CMP |
| 3 | 812 | 0.68 | 0.75 | 55 | empty |
| 4 | 470 | 0.64 | 0.77 | 41 | empty |
| 5 | 275 | 0.61 | 0.79 | 25 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1573 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 628 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- D–E · 619 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- D–B · 401 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–A · 400 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1RUN · Catabolite gene activator protein (CAP)/DNA complex + adenosine-3',5'-cyclic-monophosphate · 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 B 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 1RUN · PDBe 1RUN · UniProt P0ACJ8
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