MolNFT v1 · #30037 · protein + DNA
4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6A;17T]ICAP38 DNA
1ZRD · 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*AP*GP*AP*T)- 3': “4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6A;17T]ICAP38 DNA”. X-ray diffraction, 1 ligand (CMP), 6 pockets (best druggability…
- PDB
- 1ZRD
- 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*AP*GP*AP*T)- 3'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 31% 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*AP*GP*AP*T)- 3' | dna | 17 | — | — |
| X, Z | 5'-D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP *AP*AP*T)-3' | dna | 21 | — | — |
| A, B | Catabolite gene activator | protein | 200 | 39% helix, 31% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.76 | 0.85 | 53 | CMP |
| 2 | 920 | 0.73 | 0.77 | 56 | empty |
| 3 | 493 | 0.73 | 0.82 | 57 | CMP |
| 4 | 513 | 0.67 | 0.78 | 50 | empty |
| 5 | 429 | 0.64 | 0.78 | 45 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1565 Ų buried · 4 hydrogen bonds · protein-protein
- Y–Z · 755 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- W–X · 738 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- X–A · 414 Ų buried · 8 hydrogen bonds · protein-nucleic
- Z–B · 379 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1ZRD · 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 1ZRD · PDBe 1ZRD · UniProt P0ACJ8
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