MolNFT v1 · #137463 · protein + DNA
Transcription factor FOSB/JUND bzip domain in complex with cognate DNA, type-I crystal
5VPE · Protein fosb: “Transcription factor FOSB/JUND bzip domain in complex with cognate DNA, type-I crystal”. X-ray diffraction, 3 ligands (NA, PO4, CL), 4 pockets (best druggability 0.71). MolNFT v1 #137463 on GenesisL1: 3D structure…
- PDB
- 5VPE
- Type
- protein + DNA
- Length
- 339 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, PO4, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 95% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Protein fosb | protein | 66 | 92% helix, 0% strand | P53539 |
| D, B | Transcription factor jun-D | protein | 67 | 96% helix, 0% strand | P17535 |
| G, E | DNA (5'- D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3') | dna | 18 | — | — |
| H, 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 | — | — |
| A | Protein fosb | protein | 67 | 97% helix, 0% strand | P53539 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains C, D, G, B, E
- PO4 · Phosphate ion · ion · 3 copies · chains C, D, G, H, A, B, E, F
- CL · Chloride ion · ion · chains D, G
- EDO · 1,2-ethanediol · additive · 11 copies · chains C, D, F, G, H, A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.71 | 0.88 | 26 | PO4 |
| 2 | 253 | 0.70 | 0.86 | 29 | PO4 |
| 3 | 721 | 0.69 | 0.77 | 48 | empty |
| 4 | 131 | 0.40 | 0.75 | 19 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1213 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 831 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- E–F · 825 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–E · 395 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5VPE · Transcription factor FosB/JunD bZIP domain in complex with cognate DNA, type-I crystal · the same entry in another collection · chain F against F, 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 0.84
- P17535 · AlphaFold monomer V2.0 prediction for transcription factor jun-D (P17535) · a predicted model of the same protein · chain D against A, TM-score 0.80
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 5VPE · PDBe 5VPE · UniProt P53539 · UniProt P17535
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