Research workbench
Transcription factor FOSB/JUND bzip domain in its oxidized form, type- I crystal
Analyse Transcription factor FOSB/JUND bzip domain in its oxidized form, type- I crystal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPB
- Type
- protein
- Length
- 246 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein fosb; Transcription factor jun-D
- UniProt
- P53539, P17535
- Ligands
- CL
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Protein fosb | protein | 54 | 93% helix, 0% strand | P53539 |
| D | Transcription factor jun-D | protein | 66 | 95% helix, 0% strand | P17535 |
| A | Protein fosb | protein | 59 | 92% helix, 0% strand | P53539 |
| B | Transcription factor jun-D | protein | 67 | 96% helix, 0% strand | P17535 |
Ligands and binding sites
- CL · Chloride ion · ion · 13 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.45 | 0.76 | 18 | CL |
| 2 | 103 | 0.42 | 0.78 | 17 | CL |
| 3 | 109 | 0.38 | 0.75 | 18 | CL |
Interfaces
6 interfaces between chains.
- C–D · 1375 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1343 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 658 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 85 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 83 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VPB · Transcription factor FosB/JunD bZIP domain in its oxidized form, type-I crystal · the same entry in another collection · chain A against A, TM-score 1.00
- P17535 · AlphaFold monomer V2.0 prediction for transcription factor jun-D (P17535) · a predicted model of the same protein · chain B against A, TM-score 0.81
- P53539 · AlphaFold monomer V2.0 prediction for protein fosb (P53539) · a predicted model of the same protein · chain C against A, TM-score 0.71
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 P53539
- Every structure of UniProt P17535
- Elsewhere: RCSB PDB 5VPB · PDBe 5VPB · UniProt P53539 · UniProt P17535
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