MolNFT v1 · #7658 · protein + DNA
Crystal structure of bzip transcription factor PAP1 bound to DNA
1GD2 · DNA (5'- D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3'): “Crystal structure of bzip transcription factor PAP1 bound to DNA”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #7658 on GenesisL1: 3D structure, binding…
- PDB
- 1GD2
- Type
- protein + DNA
- Length
- 360 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3'); Transcription factor PAP1
- UniProt
- Q01663
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'- D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3') | dna | 13 | — | — |
| E | Transcription factor PAP1 | protein | 65 | 88% helix, 0% strand | Q01663 |
| F | Transcription factor PAP1 | protein | 64 | 94% helix, 0% strand | Q01663 |
| G, H | Transcription factor PAP1 | protein | 64 | 91% helix, 0% strand | Q01663 |
| I | Transcription factor PAP1 | protein | 40 | 73% helix, 0% strand | Q01663 |
| J | Transcription factor PAP1 | protein | 11 | 36% helix, 0% strand | Q01663 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.69 | 0.81 | 29 | empty |
| 2 | 647 | 0.67 | 0.77 | 47 | empty |
| 3 | 301 | 0.54 | 0.75 | 27 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1185 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1132 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- C–D · 564 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–E · 430 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1GD2 · Crystal structure of bzip transcription factor PAP1 bound to DNA · the same entry in another collection · chain J against J, TM-score 1.00
- Q01663 · AlphaFold monomer V2.0 prediction for ap-1-like transcription factor (Q01663) · a predicted model of the same protein · chain E 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 Q01663
- Elsewhere: RCSB PDB 1GD2 · PDBe 1GD2 · UniProt Q01663
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