Research workbench
Crystal structure of HSF1 DNA-binding domain in complex with 3-site hse DNA (23 bp)
Analyse Crystal structure of HSF1 DNA-binding domain in complex with 3-site hse DNA (23… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DCS
- Type
- protein + DNA
- Length
- 676 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock factor protein 1; DNA (5'- D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*T…
- UniProt
- Q00613
- Ligands
- NA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock factor protein 1 | protein | 95 | 42% helix, 16% strand | Q00613 |
| B | Heat shock factor protein 1 | protein | 102 | 40% helix, 15% strand | Q00613 |
| C | Heat shock factor protein 1 | protein | 94 | 43% helix, 13% strand | Q00613 |
| D | Heat shock factor protein 1 | protein | 95 | 43% helix, 14% strand | Q00613 |
| E | Heat shock factor protein 1 | protein | 105 | 41% helix, 14% strand | Q00613 |
| F | Heat shock factor protein 1 | protein | 93 | 45% helix, 15% strand | Q00613 |
| G, I | DNA (5'- D(*TP*GP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*GP* a)-3') | dna | 23 | — | — |
| H, J | DNA (5'- D(*AP*TP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*CP* C)-3') | dna | 23 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.81 | 0.82 | 95 | empty |
| 2 | 1127 | 0.80 | 0.82 | 92 | empty |
| 3 | 184 | 0.47 | 0.76 | 25 | empty |
| 4 | 137 | 0.46 | 0.77 | 19 | empty |
| 5 | 165 | 0.45 | 0.76 | 25 | empty |
Interfaces
23 interfaces between chains.
- G–H · 1032 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- I–J · 964 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- B–G · 464 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–J · 455 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–I · 444 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 7DCS · Crystal structure of HSF1 DNA-binding domain in complex with 3-site HSE DNA (23 bp) · the same entry in another collection · chain J against J, TM-score 1.00
- Q00613 · AlphaFold monomer V2.0 prediction for heat shock factor protein 1 (Q00613) · a predicted model of the same protein · chain A 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 Q00613
- Elsewhere: RCSB PDB 7DCS · PDBe 7DCS · UniProt Q00613
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