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Structural basis for cell type specific DNA binding of C/EBPbeta: the case of cell cycle inhibitor p15INK4b promoter
Analyse Structural basis for cell type specific DNA binding of C/EBPbeta: the case of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPZ
- Type
- protein + DNA
- Length
- 164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.487
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- CCAAT/enhancer-binding protein beta; DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*…
- UniProt
- P17676
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.487 · 4 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCAAT/enhancer-binding protein beta | protein | 64 | 92% helix, 0% strand | P17676 |
| B | CCAAT/enhancer-binding protein beta | protein | 68 | 88% helix, 0% strand | P17676 |
| C | DNA (5'-D(*AP*TP*TP*CP*TP*TP*AP*AP*GP*AP*AP*AP*GP*AP*CP*G)-3') | dna | 16 | — | — |
| D | DNA (5'-D(*TP*CP*GP*TP*CP*TP*TP*TP*CP*TP*TP*AP*AP*GP*AP*A)-3') | dna | 16 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.70 | 0.79 | 28 | empty |
| 2 | 179 | 0.51 | 0.78 | 17 | empty |
| 3 | 131 | 0.45 | 0.77 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1034 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 667 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–D · 370 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 360 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 358 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- P17676 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein beta (P17676) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P17676
- Elsewhere: RCSB PDB 7UPZ · PDBe 7UPZ · UniProt P17676
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