MolNFT v1 · #137464 · protein + DNA
Transcription factor FOSB/JUND bzip domain in complex with cognate DNA, type-II crystal
5VPF · Protein fosb: “Transcription factor FOSB/JUND bzip domain in complex with cognate DNA, type-II crystal”. X-ray diffraction, 3 ligands (NA, CL, PO4), 6 pockets (best druggability 0.70). MolNFT v1 #137464 on GenesisL1: 3D structure…
- PDB
- 5VPF
- Type
- protein + DNA
- Length
- 338 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein fosb; Transcription factor jun-D; DNA (5'…
- UniProt
- P53539, P17535
- Ligands
- NA, CL, PO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein fosb | protein | 67 | 94% helix, 0% strand | P53539 |
| B | Transcription factor jun-D | protein | 67 | 94% helix, 0% strand | P17535 |
| E, G | DNA (5'- D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3') | dna | 19 | — | — |
| F | DNA (5'- D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3') | dna | 18 | — | — |
| C | Protein fosb | protein | 64 | 92% helix, 0% strand | P53539 |
| D | Transcription factor jun-D | protein | 65 | 95% helix, 0% strand | P17535 |
| H | DNA (5'- D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3') | dna | 19 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B, E
- CL · Chloride ion · ion · 2 copies · chains A, E, B, F
- PO4 · Phosphate ion · ion · 2 copies · chains C, D, G
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, F, E, C, D, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.70 | 0.84 | 30 | EDO |
| 2 | 255 | 0.65 | 0.83 | 30 | EDO |
| 3 | 512 | 0.62 | 0.76 | 30 | empty |
| 4 | 90 | 0.49 | 0.83 | 17 | CL |
| 5 | 81 | 0.49 | 0.83 | 15 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1249 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1145 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 866 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- E–F · 835 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–E · 384 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5VPF · Transcription factor FosB/JunD bZIP domain in complex with cognate DNA, type-II crystal · the same entry in another collection · chain H against H, TM-score 1.00
- P53539 · AlphaFold monomer V2.0 prediction for protein fosb (P53539) · a predicted model of the same protein · chain A against A, TM-score 0.90
- 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 0.74
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 5VPF · PDBe 5VPF · UniProt P53539 · UniProt P17535
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