MolNFT v1 · #6663 · protein + DNA
Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide
1FJL: “Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide”. X-ray diffraction, 4 pockets (best druggability 0.77). MolNFT v1 #6663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FJL
- Type
- protein + DNA
- Length
- 224 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paired protein; DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3'); DNA…
- UniProt
- P06601
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paired protein | protein | 65 | 71% helix, 0% strand | P06601 |
| B | Paired protein | protein | 58 | 67% helix, 0% strand | P06601 |
| C | Paired protein | protein | 59 | 68% helix, 0% strand | P06601 |
| D | DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3') | dna | 14 | — | — |
| E | DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3') | dna | 14 | — | — |
| F | DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3') | dna | 14 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.77 | 0.95 | 22 | empty |
| 2 | 117 | 0.46 | 0.79 | 19 | empty |
| 3 | 142 | 0.43 | 0.76 | 20 | empty |
| 4 | 135 | 0.43 | 0.76 | 18 | empty |
Interfaces
11 interfaces between chains.
- D–E · 590 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–D · 586 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–F · 564 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–E · 509 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 503 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1FJL · Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide · the same entry in another collection · chain F against F, TM-score 1.00
- P06601 · AlphaFold monomer V2.0 prediction for segmentation protein paired (P06601) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P06601
- Elsewhere: RCSB PDB 1FJL · PDBe 1FJL · UniProt P06601
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.