MolNFT v1 · #110274 · protein + DNA
Homodimer of tale type homeobox transcription factor MEIS1 complexes with specific DNA
4XRM · DNA (5'- D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP…: “Homodimer of tale type homeobox transcription factor MEIS1 complexes with specific DNA”. X-ray diffraction, 2 pockets (best druggability 0.57). MolNFT v1 #110274 on…
- PDB
- 4XRM
- Type
- protein + DNA
- Length
- 157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*G)-3'); DNA (5'…
- UniProt
- O14770
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'- D(P*AP*GP*CP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*AP*G)-3') | dna | 17 | — | — |
| L | DNA (5'- D(P*TP*CP*TP*TP*GP*AP*CP*AP*GP*CP*TP*GP*TP*CP*AP*GP*C)-3') | dna | 17 | — | — |
| A | Homeobox protein MEIS2 | protein | 59 | 69% helix, 0% strand | O14770 |
| B | Homeobox protein MEIS2 | protein | 64 | 67% helix, 0% strand | O14770 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains M, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.57 | 0.78 | 23 | TRS |
| 2 | 82 | 0.29 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- M–L · 785 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- M–B · 366 Ų buried · 8 hydrogen bonds · protein-nucleic
- L–A · 358 Ų buried · 6 hydrogen bonds · protein-nucleic
- M–A · 318 Ų buried · 7 hydrogen bonds · protein-nucleic
- L–B · 318 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4XRM · homodimer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA · the same entry in another collection · chain M against M, TM-score 1.00
- O14770 · AlphaFold monomer V2.0 prediction for homeobox protein MEIS2 (O14770) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O14770
- Elsewhere: RCSB PDB 4XRM · PDBe 4XRM · UniProt O14770
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