Research workbench
C-terminal bzip domain of human C/EBPBETA bound to DNA with consensus recognition with gt mismatch
Analyse C-terminal bzip domain of human C/EBPBETA bound to DNA with consensus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L4V
- Type
- protein + DNA
- Length
- 167 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCAAT/ENHANCER-binding protein beta; DNA strand 1; DNA strand 2
- UniProt
- P17676
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCAAT/ENHANCER-binding protein beta | protein | 66 | 88% helix, 0% strand | P17676 |
| B | CCAAT/ENHANCER-binding protein beta | protein | 69 | 88% helix, 0% strand | P17676 |
| C | DNA strand 1 | dna | 16 | — | — |
| D | DNA strand 2 | dna | 16 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.69 | 0.79 | 34 | EDO |
| 2 | 56 | 0.32 | 0.77 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1010 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 714 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- A–C · 431 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 413 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 368 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 7L4V · C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Consensus Recognition with GT… · 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 0.88
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 7L4V · PDBe 7L4V · UniProt P17676
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