Research workbench
Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices
Analyse Solution structure of a specific DNA complex of the myb DNA-binding domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MSF
- Type
- protein + DNA
- Length
- 127 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)- 3'); DNA…
- UniProt
- P06876
- Pockets
- 4 · best druggability 0.41
Structure
solution nmr · 3 distinct chains · 47% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*CP*TP*AP*AP*CP*TP*GP*AP*CP*AP*CP*AP*CP*AP*T)- 3') | dna | 11 | — | — |
| B | DNA (5'-D(*AP*TP*GP*TP*GP*TP*GP*TP*CP*AP*GP*TP*TP*AP*GP*G)- 3') | dna | 11 | — | — |
| C | C-myb DNA-binding domain | protein | 105 | 47% helix, 0% strand | P06876 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.41 | 0.78 | 17 | empty |
| 2 | 57 | 0.32 | 0.77 | 16 | empty |
| 3 | 77 | 0.31 | 0.74 | 13 | empty |
| 4 | 51 | 0.27 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 751 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 633 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 507 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 1MSF · Solution structure of a specific DNA complex of the myb DNA-binding domain with… · the same entry in another collection · chain A against A, TM-score 1.00
- P06876 · AlphaFold monomer V2.0 prediction for transcriptional activator myb (P06876) · a predicted model of the same protein · chain C against A, TM-score 0.76
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 P06876
- Elsewhere: RCSB PDB 1MSF · PDBe 1MSF · UniProt P06876
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