Research workbench
Crystal structure of myod bhlh domain bound to DNA: perspectives on DNA recognition and implications for transcriptional activation
Analyse Crystal structure of myod bhlh domain bound to DNA: perspectives on DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MDY
- Type
- protein + DNA
- Length
- 310 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3'); Protein (myod bhlh domain)
- UniProt
- P10085
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H | DNA (5'- D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3') | dna | 14 | — | — |
| A | Protein (myod bhlh domain) | protein | 68 | 66% helix, 0% strand | P10085 |
| B, C, D | Protein (myod bhlh domain) | protein | 62 | 74% helix, 0% strand | P10085 |
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 | 210 | 0.80 | 0.94 | 28 | empty |
| 2 | 168 | 0.79 | 0.95 | 24 | empty |
| 3 | 99 | 0.45 | 0.80 | 16 | empty |
| 4 | 131 | 0.44 | 0.77 | 21 | empty |
| 5 | 105 | 0.44 | 0.79 | 17 | empty |
Interfaces
16 interfaces between chains.
- C–D · 888 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 859 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 634 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- G–H · 631 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- E–B · 479 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1MDY · Crystal structure of myod bhlh domain bound to DNA: perspectives on DNA recognition and… · the same entry in another collection · chain D against D, TM-score 1.00
- P10085 · AlphaFold monomer V2.0 prediction for myoblast determination protein 1 (P10085) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P10085
- Elsewhere: RCSB PDB 1MDY · PDBe 1MDY · UniProt P10085
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