MolNFT v1 · #18607 · protein + DNA
Crystal structure of HOXA9 and PBX1 homeodomains bound to DNA
1PUF · 5'- D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP…: “Crystal structure of HOXA9 and PBX1 homeodomains bound to DNA”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #18607 on GenesisL1: 3D structure…
- PDB
- 1PUF
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP *T)-3'; 5'…
- UniProt
- P09631, P40424
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'- D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*TP*AP*CP*GP*AP*CP*GP*CP *T)-3' | dna | 20 | — | — |
| E | 5'- D(*TP*AP*GP*CP*GP*TP*CP*GP*TP*AP*AP*AP*TP*CP*AP*TP*AP*GP*AP *G)-3' | dna | 20 | — | — |
| A | Homeobox protein hox-A9 | protein | 77 | 60% helix, 0% strand | P09631 |
| B | Pre-B-cell leukemia transcription factor-1 | protein | 73 | 62% helix, 0% strand | P40424 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.73 | 0.80 | 56 | empty |
| 2 | 124 | 0.45 | 0.78 | 17 | empty |
| 3 | 96 | 0.40 | 0.77 | 13 | empty |
| 4 | 50 | 0.34 | 0.79 | 12 | empty |
| 5 | 69 | 0.34 | 0.77 | 14 | empty |
Interfaces
6 interfaces between chains.
- D–E · 867 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- E–A · 725 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–A · 669 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–B · 549 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–B · 421 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1PUF · Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA · the same entry in another collection · chain D against D, TM-score 1.00
- P40424 · AlphaFold monomer V2.0 prediction for pre-B-cell leukemia transcription factor 1 (P40424) · a predicted model of the same protein · chain B against A, TM-score 0.92
- P09631 · AlphaFold monomer V2.0 prediction for homeobox protein hox-A9 (P09631) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P09631
- Every structure of UniProt P40424
- Elsewhere: RCSB PDB 1PUF · PDBe 1PUF · UniProt P09631 · UniProt P40424
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