MolNFT v1 · #117695 · protein + DNA
HOXB13-MEIS1 heterodimer bound to DNA
5EG0 · Homeobox protein MEIS2: “HOXB13-MEIS1 heterodimer bound to DNA”. X-ray diffraction, 5 pockets (best druggability 0.64). MolNFT v1 #117695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EG0
- Type
- protein + DNA
- Length
- 153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein MEIS2; DNA (5'- D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)…
- UniProt
- O14770, Q92826
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein MEIS2 | protein | 56 | 66% helix, 0% strand | O14770 |
| D | DNA (5'- D(P*GP*TP*TP*GP*AP*CP*AP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*G)-3') | dna | 18 | — | — |
| E | DNA (5'- D(*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*TP*GP*TP*CP*AP*AP*C)-3') | dna | 18 | — | — |
| B | Homeobox protein hox-B13 | protein | 61 | 56% helix, 0% strand | Q92826 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.64 | 0.88 | 20 | empty |
| 2 | 217 | 0.51 | 0.77 | 23 | empty |
| 3 | 107 | 0.46 | 0.79 | 17 | empty |
| 4 | 102 | 0.37 | 0.75 | 13 | empty |
| 5 | 79 | 0.36 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–E · 751 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- D–B · 646 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–B · 519 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 362 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–E · 335 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5EG0 · HOXB13-MEIS1 heterodimer bound to DNA · the same entry in another collection · chain A against A, 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
- 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 0.92
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
- Every structure of UniProt Q92826
- Elsewhere: RCSB PDB 5EG0 · PDBe 5EG0 · UniProt O14770 · UniProt Q92826
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