Research workbench
Crystal structure of the csl-notch-mastermind ternary complex bound to DNA
Analyse Crystal structure of the csl-notch-mastermind ternary complex bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FO1
- Type
- protein + DNA
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'; 5'…
- UniProt
- Q09260, P14585
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'- D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3' | dna | 15 | — | — |
| C | 5'- D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3' | dna | 15 | — | — |
| A | Lin-12 and glp-1 phenotype protein 1, isoform B | protein | 439 | 9% helix, 42% strand | — |
| D | Protein lag-3 | protein | 63 | 81% helix, 0% strand | Q09260 |
| E | Lin-12 protein | protein | 297 | 43% helix, 1% strand | P14585 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.83 | 0.84 | 123 | empty |
| 2 | 526 | 0.76 | 0.84 | 43 | empty |
| 3 | 740 | 0.73 | 0.79 | 62 | empty |
| 4 | 186 | 0.54 | 0.79 | 25 | empty |
| 5 | 188 | 0.50 | 0.77 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–E · 2679 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 1368 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1104 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 600 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- B–A · 553 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2FO1 · Crystal Structure of the CSL-Notch-Mastermind ternary complex bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P14585 · AlphaFold monomer V2.0 prediction for protein lin-12 (P14585) · a predicted model of the same protein · chain E against A, TM-score 0.92
- Q09260 · AlphaFold monomer V2.0 prediction for protein lag-3 (Q09260) · a predicted model of the same protein · chain D against A, TM-score 0.87
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 Q09260
- Every structure of UniProt P14585
- Elsewhere: RCSB PDB 2FO1 · PDBe 2FO1 · UniProt Q09260 · UniProt P14585
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