Research workbench
MEF2 CHIMERA/DNA complex
Analyse MEF2 CHIMERA/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BYY
- Type
- protein + DNA
- Length
- 417 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MEF2 chimera; DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3'); DNA…
- UniProt
- Q02078, Q02080
- Ligands
- 1PG, TCE
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | MEF2 chimera | protein | 91 | 48% helix, 16% strand | Q02078, Q02080 |
| D | MEF2 chimera | protein | 89 | 47% helix, 17% strand | Q02078, Q02080 |
| K, E | DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3') | dna | 14 | — | — |
| L | DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)- 3') | dna | 14 | — | — |
| F | DNA (5'-D(P*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)- 3') | dna | 13 | — | — |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B, D
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.69 | 0.85 | 42 | empty |
| 2 | 240 | 0.52 | 0.76 | 27 | empty |
| 3 | 198 | 0.48 | 0.75 | 27 | empty |
| 4 | 101 | 0.48 | 0.81 | 21 | empty |
| 5 | 85 | 0.48 | 0.82 | 22 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3168 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3157 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 619 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–F · 591 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–L · 518 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6BYY · MEF2 CHIMERA/DNA Complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q02078 · AlphaFold monomer V2.0 prediction for myocyte-specific enhancer factor 2A (Q02078) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q02080 · AlphaFold monomer V2.0 prediction for myocyte-specific enhancer factor 2B (Q02080) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q02078
- Every structure of UniProt Q02080
- Elsewhere: RCSB PDB 6BYY · PDBe 6BYY · UniProt Q02078 · UniProt Q02080
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.