Research workbench
Crystal structure of MYC3 N-terminal jaz-binding domain [44-238] from arabidopsis
Analyse Crystal structure of MYC3 N-terminal jaz-binding domain [44-238] from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQW
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor MYC3
- UniProt
- Q9FIP9
- Ligands
- CA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor MYC3 | protein | 169 | 41% helix, 28% strand | Q9FIP9 |
| B | Transcription factor MYC3 | protein | 159 | 43% helix, 24% strand | Q9FIP9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.74 | 0.81 | 50 | empty |
| 2 | 131 | 0.55 | 0.82 | 23 | empty |
| 3 | 174 | 0.48 | 0.76 | 24 | empty |
| 4 | 84 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4RQW · Crystal structure of Myc3 N-terminal JAZ-binding domain [44-238] from Arabidopsis · 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 A 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 Q9FIP9
- Elsewhere: RCSB PDB 4RQW · PDBe 4RQW · UniProt Q9FIP9
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