Research workbench
Crystal structure of MYC3(5-242) fragment in complex with JAZ9(218- 239) peptide
Analyse Crystal structure of MYC3(5-242) fragment in complex with JAZ9(218- 239) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YWC
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor MYC3; Protein tify 7
- UniProt
- Q9FIP9, Q8W4J8
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor MYC3 | protein | 179 | 43% helix, 23% strand | Q9FIP9 |
| C, D | Protein tify 7 | protein | 22 | 77% helix, 0% strand | Q8W4J8 |
| B | Transcription factor MYC3 | protein | 179 | 41% helix, 25% strand | Q9FIP9 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.77 | 0.80 | 85 | empty |
| 2 | 209 | 0.55 | 0.78 | 29 | empty |
| 3 | 118 | 0.50 | 0.80 | 17 | empty |
| 4 | 149 | 0.49 | 0.77 | 18 | empty |
| 5 | 117 | 0.38 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 871 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 840 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 414 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 137 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4YWC · Crystal structure of Myc3(5-242) fragment in complex with Jaz9(218-239) peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FIP9 · AlphaFold monomer V2.0 prediction for transcription factor MYC3 (Q9FIP9) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q8W4J8 · AlphaFold monomer V2.0 prediction for protein tify 7 (Q8W4J8) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 Q9FIP9
- Every structure of UniProt Q8W4J8
- Elsewhere: RCSB PDB 4YWC · PDBe 4YWC · UniProt Q9FIP9 · UniProt Q8W4J8
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