Research workbench
Crystal structure of two HMGB1 box a domains cooperating to underwind and kink a DNA
Analyse Crystal structure of two HMGB1 box a domains cooperating to underwind and kink… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QR9
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High mobility group protein B1; DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')
- UniProt
- P63159
- Ligands
- MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | High mobility group protein B1 | protein | 75 | 71% helix, 0% strand | P63159 |
| C, D, E, F | DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.67 | 0.78 | 58 | empty |
| 2 | 193 | 0.54 | 0.80 | 18 | MG |
| 3 | 71 | 0.35 | 0.76 | 13 | empty |
| 4 | 64 | 0.30 | 0.74 | 14 | empty |
Interfaces
14 interfaces between chains.
- A–C · 493 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 491 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 481 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 468 Ų buried · 5 hydrogen bonds · protein-nucleic
- C–D · 459 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 4QR9 · Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA · the same entry in another collection · chain C against C, TM-score 1.00
- P63159 · AlphaFold monomer V2.0 prediction for high mobility group protein B1 (P63159) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P63159
- Elsewhere: RCSB PDB 4QR9 · PDBe 4QR9 · UniProt P63159
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