MolNFT v1 · #30038 · protein + DNA
4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6G;17C]ICAP38 DNA
1ZRE · 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)- 3': “4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6G;17C]ICAP38 DNA”. X-ray diffraction, 1 ligand (CMP), 10 pockets (best druggability…
- PDB
- 1ZRE
- Type
- protein + DNA
- Length
- 476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)- 3'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W, Y | 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*GP*GP*AP*T)- 3' | dna | 17 | — | — |
| X, Z | 5'-D(*CP*TP*AP*GP*AP*TP*CP*CP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP *AP*AP*T)-3' | dna | 21 | — | — |
| A, B | Catabolite gene activator | protein | 200 | 40% helix, 30% 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.76 | 0.83 | 66 | CMP |
| 2 | 880 | 0.73 | 0.78 | 59 | empty |
| 3 | 386 | 0.73 | 0.84 | 43 | CMP |
| 4 | 356 | 0.61 | 0.78 | 36 | empty |
| 5 | 276 | 0.56 | 0.77 | 32 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1545 Ų buried · 6 hydrogen bonds · protein-protein
- W–X · 749 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- Y–Z · 748 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- Z–B · 442 Ų buried · 8 hydrogen bonds · protein-nucleic
- X–A · 433 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1ZRE · 4 crystal structures of CAP-DNA with all base-pair substitutions at position 6… · 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 1ZRE · PDBe 1ZRE · UniProt P0ACJ8
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