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Structure of the AT-Hook 1 peptide from the mammalian HMGA protein in complex with DNA
Analyse Structure of the AT-Hook 1 peptide from the mammalian HMGA protein in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CPG
- Type
- protein + DNA
- Length
- 90 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Molecule
- DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3'); High mobility group protein…
- UniProt
- P17096
- Ligands
- MG
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · resolution 1.4 · 5 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3') | dna | 12 | — | — |
| B, C | DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*AP*AP*CP*G)-3') | dna | 11 | — | — |
| G | High mobility group protein HMG-I/HMG-Y | protein | 9 | 0% helix, 0% strand | P17096 |
| H | High mobility group protein HMG-I/HMG-Y | protein | 6 | 0% helix, 0% strand | P17096 |
| I | High mobility group protein HMG-I/HMG-Y | protein | 5 | 0% helix, 0% strand | P17096 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.78 | 26 | empty |
| 2 | 61 | 0.32 | 0.76 | 10 | empty |
Interfaces
21 interfaces between chains.
- A–B · 450 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- C–D · 444 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- E–F · 435 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- F–G · 246 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 242 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- P17096 · AlphaFold monomer V2.0 prediction for high mobility group protein hmg-I/HMG-Y (P17096) · a predicted model of the same protein · chain I against A, TM-score 0.81
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 P17096
- Elsewhere: RCSB PDB 8CPG · PDBe 8CPG · UniProt P17096
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