MolNFT v1 · #4227 · protein + DNA
Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective dimerization and DNA binding
1DH3 · DNA (5'- D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*…: “Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective dimerization and DNA…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best…
- PDB
- 1DH3
- Type
- protein + DNA
- Length
- 152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)- 3')…
- UniProt
- Q01147
- Ligands
- MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA (5'- D(*CP*CP*TP*TP*GP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*CP*AP*AP*G)- 3') | dna | 21 | — | — |
| A, C | Transcription factor creb | protein | 55 | 87% helix, 0% strand | Q01147 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.71 | 0.84 | 31 | MG |
| 2 | 150 | 0.44 | 0.76 | 15 | empty |
| 3 | 62 | 0.34 | 0.78 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–C · 994 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 911 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- B–A · 416 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–C · 414 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–A · 240 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 1DH3 · Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective… · the same entry in another collection · chain B against B, TM-score 1.00
- Q01147 · AlphaFold monomer V2.0 prediction for cyclic AMP-responsive element- binding protein 1… · a predicted model of the same protein · chain C against A, TM-score 0.87
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 Q01147
- Elsewhere: RCSB PDB 1DH3 · PDBe 1DH3 · UniProt Q01147
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