Research workbench
4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6C;17G]ICAP38 DNA
Analyse 4 crystal structures of cap-DNA with all base-pair substitutions at position 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZRF
- 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*CP*GP*AP*T)- 3'…
- UniProt
- P0ACJ8
- Ligands
- CMP
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)- 3' | dna | 15 | — | — |
| X, Z | 5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP *AP*AP*T)-3' | dna | 21 | — | — |
| Y | 5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)- 3' | dna | 16 | — | — |
| A | Catabolite gene activator | protein | 203 | 38% helix, 31% strand | P0ACJ8 |
| B | Catabolite gene activator | protein | 200 | 39% helix, 31% strand | P0ACJ8 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 4 copies · chains A, B, X, Z
- DIO · 1,4-diethylene dioxide · additive · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.77 | 0.81 | 76 | CMP, DIO |
| 2 | 789 | 0.76 | 0.80 | 78 | CMP, DIO |
| 3 | 1072 | 0.76 | 0.79 | 59 | CMP |
| 4 | 111 | 0.46 | 0.79 | 14 | empty |
| 5 | 99 | 0.44 | 0.79 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1553 Ų buried · 8 hydrogen bonds · protein-protein
- Y–Z · 707 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- W–X · 685 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- X–A · 476 Ų buried · 9 hydrogen bonds · protein-nucleic
- Z–B · 423 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1ZRF · 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 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 1ZRF · PDBe 1ZRF · UniProt P0ACJ8
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