MolNFT v1 · #156414 · protein + DNA
X-ray crystal structure of tandemly connected engrailed homeodomains (ehd) with R53A mutations and DNA complex
6M3D · DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3'): “X-ray crystal structure of tandemly connected engrailed homeodomains (ehd) with R53A mutations and DNA complex”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability…
- PDB
- 6M3D
- Type
- protein + DNA
- Length
- 132 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3'); DNA…
- UniProt
- P02836
- Ligands
- NA
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3') | dna | 12 | — | — |
| B | DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3') | dna | 12 | — | — |
| C | Segmentation polarity homeobox protein engrailed, segmentation polarity homeobox protein engrailed | protein | 108 | 72% helix, 0% strand | P02836 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.57 | 0.77 | 37 | empty |
| 2 | 312 | 0.56 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 663 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 516 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- B–C · 335 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6M3D · X-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A… · 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 0.52
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 6M3D · PDBe 6M3D · UniProt P02836
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.