MolNFT v1 · #134303 · protein + DNA
Human C-jun DNA binding domain homodimer in complex with methylated DNA
5T01 · DNA (5'- D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP…: “Human C-jun DNA binding domain homodimer in complex with methylated DNA”. X-ray diffraction, 2 pockets (best druggability 0.72). MolNFT v1 #134303 on GenesisL1: 3D…
- PDB
- 5T01
- Type
- protein + DNA
- Length
- 161 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP*AP*T)-3'); DNA…
- UniProt
- P05412
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(P*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*GP*TP*CP*CP*AP*T)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*AP*AP*TP*GP*GP*AP*(5CM) P*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*G)-3') | dna | 19 | — | — |
| A, B | Transcription factor ap-1 | protein | 62 | 90% helix, 0% strand | P05412 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.72 | 0.82 | 47 | empty |
| 2 | 141 | 0.52 | 0.80 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1081 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 835 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- C–B · 437 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 336 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–B · 317 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5T01 · Human c-Jun DNA binding domain homodimer in complex with methylated DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P05412 · AlphaFold monomer V2.0 prediction for transcription factor ap-1 (P05412) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P05412
- Elsewhere: RCSB PDB 5T01 · PDBe 5T01 · UniProt P05412
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