Research workbench
Crystal structure of C/EBPBETA bzip homodimer K269A mutant bound to a high affinity DNA fragment
Analyse Crystal structure of C/EBPBETA bzip homodimer K269A mutant bound to a high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E43
- Type
- protein + DNA
- Length
- 158 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)- 3'); DNA…
- UniProt
- P17676
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)- 3') | dna | 16 | — | — |
| D | DNA (5'- D(P*DAP*DAP*DTP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DCP*DT)- 3') | dna | 16 | — | — |
| A | CCAAT/ENHANCER-binding protein beta | protein | 62 | 94% helix, 0% strand | P17676 |
| B | CCAAT/ENHANCER-binding protein beta | protein | 64 | 95% helix, 0% strand | P17676 |
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 | 508 | 0.68 | 0.79 | 33 | empty |
| 2 | 100 | 0.44 | 0.79 | 12 | empty |
| 3 | 118 | 0.43 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 663 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- C–A · 396 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–B · 390 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–A · 344 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2E43 · Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound to A High Affinity DNA… · the same entry in another collection · chain C against C, TM-score 1.00
- 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 2E43 · PDBe 2E43 · UniProt P17676
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