MolNFT v1 · #10884 · protein + DNA
Catabolite gene activator protein (CAP)/DNA complex + adenosine-3',5'- cyclic-monophosphate
1J59 · 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3': “Catabolite gene activator protein (CAP)/DNA complex + adenosine-3',5'- cyclic-monophosphate”. X-ray diffraction, 1 ligand (CMP), 9 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 1J59
- Type
- protein + DNA
- Length
- 458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3' | dna | 14 | — | — |
| D, F | 5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )- 3' | dna | 17 | — | — |
| A | Catabolite gene activator protein (cap) | protein | 199 | 38% helix, 27% strand | P0ACJ8 |
| B | Catabolite gene activator protein (cap) | protein | 197 | 41% helix, 27% 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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.76 | 0.84 | 57 | CMP |
| 2 | 135 | 0.75 | 0.93 | 27 | CMP |
| 3 | 292 | 0.69 | 0.84 | 25 | empty |
| 4 | 725 | 0.69 | 0.77 | 45 | empty |
| 5 | 415 | 0.62 | 0.77 | 35 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1574 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 631 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–E · 630 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- F–A · 420 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–B · 388 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1J59 · 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 0.98
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 1J59 · PDBe 1J59 · UniProt P0ACJ8
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