MolNFT v1 · #38911 · protein + DNA
Engrailed homeodomain Q50K variant DNA complex
2HDD · DNA (5'- D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*…: “Engrailed homeodomain Q50K variant DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.57). MolNFT v1 #38911 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2HDD
- Type
- protein + DNA
- Length
- 153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)- 3'); DNA…
- UniProt
- P02836
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)- 3') | dna | 21 | — | — |
| A | Protein (engrailed homeodomain Q50K) | protein | 55 | 73% helix, 0% strand | P02836 |
| B | Protein (engrailed homeodomain Q50K) | protein | 56 | 70% helix, 0% strand | P02836 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.57 | 0.80 | 23 | empty |
| 2 | 152 | 0.44 | 0.75 | 21 | empty |
| 3 | 125 | 0.36 | 0.73 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 909 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- D–A · 432 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 417 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 327 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–B · 262 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
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 P02836
- Elsewhere: RCSB PDB 2HDD · PDBe 2HDD · UniProt P02836
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