Research workbench
Crystal structure of HSF2 DNA-binding domain in complex with 3-site hse DNA (21 bp)
Analyse Crystal structure of HSF2 DNA-binding domain in complex with 3-site hse DNA (21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DCU
- Type
- protein + DNA
- Length
- 337 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock factor protein 2; DNA (5'- D(*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*C…
- UniProt
- Q03933
- Ligands
- NA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock factor protein 2 | protein | 101 | 42% helix, 12% strand | Q03933 |
| B | Heat shock factor protein 2 | protein | 102 | 41% helix, 14% strand | Q03933 |
| C | Heat shock factor protein 2 | protein | 92 | 46% helix, 14% strand | Q03933 |
| D | DNA (5'- D(*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*G)- 3') | dna | 21 | — | — |
| E | DNA (5'- D(*AP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.82 | 0.83 | 90 | empty |
| 2 | 199 | 0.57 | 0.80 | 21 | empty |
| 3 | 196 | 0.48 | 0.76 | 28 | empty |
Interfaces
10 interfaces between chains.
- D–E · 926 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- B–D · 503 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 480 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–E · 441 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 437 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7DCU · Crystal structure of HSF2 DNA-binding domain in complex with 3-site HSE DNA (21 bp) · the same entry in another collection · chain E against E, TM-score 1.00
- Q03933 · AlphaFold monomer V2.0 prediction for heat shock factor protein 2 (Q03933) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q03933
- Elsewhere: RCSB PDB 7DCU · PDBe 7DCU · UniProt Q03933
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