Research workbench
Structure of HOXB13 complex with methylated DNA
Analyse Structure of HOXB13 complex with methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EF6
- Type
- protein + DNA
- Length
- 390 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein hox-B13; DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)…
- UniProt
- Q92826
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Homeobox protein hox-B13 | protein | 61 | 67% helix, 0% strand | Q92826 |
| C, D, H, K | DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*GP*GP*TP*CP*C)-3') | dna | 18 | — | — |
| F, E, I, L | DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') | dna | 18 | — | — |
| G, J | Homeobox protein hox-B13 | protein | 62 | 65% helix, 0% strand | Q92826 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.84 | 0.85 | 79 | empty |
| 2 | 908 | 0.84 | 0.86 | 64 | empty |
| 3 | 105 | 0.56 | 0.85 | 25 | empty |
| 4 | 61 | 0.52 | 0.87 | 15 | empty |
| 5 | 74 | 0.49 | 0.84 | 17 | empty |
Interfaces
32 interfaces between chains.
- C–F · 784 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- K–L · 777 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- H–I · 777 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- D–E · 772 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–C · 623 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 5EF6 · Structure of HOXB13 complex with methylated DNA · the same entry in another collection · chain E against E, TM-score 1.00
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 Q92826
- Elsewhere: RCSB PDB 5EF6 · PDBe 5EF6 · UniProt Q92826
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