MolNFT v1 · #117620 · protein + DNA
Structure of HOXB13-DNA(TCG) complex
5EDN · Homeobox protein hox-B13: “Structure of HOXB13-DNA(TCG) complex”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #117620 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EDN
- Type
- protein + DNA
- Length
- 394 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homeobox protein hox-B13; DNA (5'- D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*…
- UniProt
- Q92826
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homeobox protein hox-B13 | protein | 60 | 70% helix, 0% strand | Q92826 |
| B, J | Homeobox protein hox-B13 | protein | 61 | 67% helix, 0% strand | Q92826 |
| C, D, H, K | DNA (5'- D(P*GP*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*CP*GP*AP*GP*GP*TP*CP*C)-3') | dna | 19 | — | — |
| E, F, I, L | DNA (5'- D(P*GP*GP*AP*CP*CP*TP*CP*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*AP*C)-3') | dna | 19 | — | — |
| G | Homeobox protein hox-B13 | protein | 60 | 67% helix, 0% strand | Q92826 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.71 | 0.79 | 66 | empty |
| 2 | 639 | 0.69 | 0.78 | 65 | empty |
| 3 | 145 | 0.54 | 0.81 | 18 | empty |
| 4 | 109 | 0.44 | 0.78 | 19 | empty |
| 5 | 164 | 0.44 | 0.75 | 15 | empty |
Interfaces
25 interfaces between chains.
- C–F · 836 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- H–I · 831 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- K–L · 773 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–E · 769 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–C · 621 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5EDN · Structure of HOXB13-DNA(TCG) complex · the same entry in another collection · chain L against L, 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 5EDN · PDBe 5EDN · UniProt Q92826
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