MolNFT v1 · #156812 · protein + DNA
V285A mutant of the C-terminal bzip domain of human C/EBPBETA with 16BP methylated oligonucleotide containing consensus recognition sequence
6MG3 · CCAAT/ENHANCER-binding protein beta: “V285A mutant of the C-terminal bzip domain of human C/EBPBETA with 16BP methylated oligonucleotide containing…”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #156812 on…
- PDB
- 6MG3
- Type
- protein + DNA
- Length
- 164 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCAAT/ENHANCER-binding protein beta; 16-bp methylated oligonucleotide
- UniProt
- P17676
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCAAT/ENHANCER-binding protein beta | protein | 64 | 89% helix, 0% strand | P17676 |
| B | CCAAT/ENHANCER-binding protein beta | protein | 68 | 90% helix, 0% strand | P17676 |
| C, D | 16-bp methylated oligonucleotide | dna | 16 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains C, D
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 | 423 | 0.68 | 0.80 | 35 | empty |
| 2 | 122 | 0.45 | 0.78 | 13 | empty |
| 3 | 84 | 0.34 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1008 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 709 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–C · 423 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 393 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 356 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6MG3 · V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated… · the same entry in another collection · chain A against A, 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 0.89
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 6MG3 · PDBe 6MG3 · UniProt P17676
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