Research workbench
Structure of HOXB13-DNA(CAA) complex
Analyse Structure of HOXB13-DNA(CAA) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EEA
- Type
- protein + DNA
- Length
- 391 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3'); DNA (5'…
- UniProt
- Q92826
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C, H, K | DNA (5'- D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3') | dna | 18 | — | — |
| E, F, I, L | DNA (5'- D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') | dna | 18 | — | — |
| B, J | Homeobox protein hox-B13 | protein | 61 | 70% helix, 0% strand | Q92826 |
| A | Homeobox protein hox-B13 | protein | 62 | 69% helix, 0% strand | Q92826 |
| G | Homeobox protein hox-B13 | protein | 63 | 67% helix, 0% strand | Q92826 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.74 | 0.78 | 65 | empty |
| 2 | 562 | 0.67 | 0.77 | 61 | empty |
| 3 | 280 | 0.54 | 0.76 | 29 | empty |
| 4 | 205 | 0.52 | 0.78 | 21 | empty |
| 5 | 181 | 0.50 | 0.78 | 29 | empty |
Interfaces
23 interfaces between chains.
- D–E · 824 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–F · 786 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- H–I · 782 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- K–L · 774 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- C–A · 592 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5EEA · Structure of HOXB13-DNA(CAA) complex · the same entry in another collection · chain J against J, 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 5EEA · PDBe 5EEA · UniProt Q92826
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