Research workbench
HOXB13-MEIS1 heterodimer bound to methylated DNA
Analyse HOXB13-MEIS1 heterodimer bound to methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EGO
- Type
- protein + DNA
- Length
- 156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein MEIS1; DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM)…
- UniProt
- O00470, Q92826
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein MEIS1 | protein | 57 | 70% helix, 0% strand | O00470 |
| D | DNA (5'-D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*GP*G)-3') | dna | 18 | — | — |
| E | DNA (5'-D(*CP*CP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3') | dna | 18 | — | — |
| B | Homeobox protein hox-B13 | protein | 63 | 60% helix, 0% strand | Q92826 |
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 | 317 | 0.61 | 0.79 | 41 | empty |
| 2 | 71 | 0.32 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–E · 804 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–B · 571 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–B · 535 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–E · 375 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 358 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5EGO · HOXB13-MEIS1 heterodimer bound to methylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
- O00470 · AlphaFold monomer V2.0 prediction for homeobox protein MEIS1 (O00470) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q92826 · AlphaFold monomer V2.0 prediction for homeobox protein hox-B13 (Q92826) · 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 O00470
- Every structure of UniProt Q92826
- Elsewhere: RCSB PDB 5EGO · PDBe 5EGO · UniProt O00470 · UniProt Q92826
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