Research workbench
Crystal structure of an engrailed homeodomain-DNA complex at 2.8 ångströms resolution: a framework for understanding homeodomain-DNA interactions
Analyse Crystal structure of an engrailed homeodomain-DNA complex at 2.8 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDD
- Type
- protein + DNA
- Length
- 156 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*TP*AP*C P*CP*TP*AP*A)- 3'); DNA…
- UniProt
- P02836
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*C P*CP*TP*AP*A)- 3') | dna | 21 | — | — |
| B | DNA (5'- D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)- 3') | dna | 21 | — | — |
| C, D | Protein (engrailed homeodomain) | protein | 57 | 63% helix, 0% strand | P02836 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.61 | 0.82 | 19 | empty |
| 2 | 56 | 0.28 | 0.74 | 10 | empty |
| 3 | 56 | 0.27 | 0.73 | 11 | empty |
| 4 | 53 | 0.23 | 0.72 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 897 Ų buried · 93 hydrogen bonds · nucleic-nucleic
- A–C · 501 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 499 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 284 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–D · 212 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1HDD · Crystal structure of an engrailed homeodomain-DNA complex at 2.8 ångströms resolution: a… · the same entry in another collection · chain A against A, TM-score 1.00
- P02836 · AlphaFold monomer V2.0 prediction for segmentation polarity homeobox protein engrailed… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 1HDD · PDBe 1HDD · UniProt P02836
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