Research workbench
Crystal structure of heat shock FACTOR1-dbd complex with ds-DNA and ttt
Analyse Crystal structure of heat shock FACTOR1-dbd complex with ds-DNA and ttt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HDN
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock factor protein 1; DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
- UniProt
- Q00613
- Ligands
- NA
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock factor protein 1 | protein | 101 | 42% helix, 17% strand | Q00613 |
| B | Heat shock factor protein 1 | protein | 99 | 41% helix, 17% strand | Q00613 |
| E, F, G, H | DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3') | dna | 12 | — | — |
| C | Heat shock factor protein 1 | protein | 107 | 38% helix, 16% strand | Q00613 |
| D | Heat shock factor protein 1 | protein | 94 | 45% helix, 15% strand | Q00613 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.66 | 0.75 | 56 | empty |
| 2 | 395 | 0.63 | 0.78 | 24 | empty |
| 3 | 255 | 0.57 | 0.78 | 37 | empty |
| 4 | 185 | 0.55 | 0.80 | 31 | CIT |
| 5 | 198 | 0.47 | 0.75 | 20 | empty |
Interfaces
12 interfaces between chains.
- C–D · 802 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 799 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 525 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- E–F · 515 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–C · 471 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5HDN · Crystal structure of heat shock factor1-DBD complex with ds-DNA and TtT · the same entry in another collection · chain H against H, 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 D against A, TM-score 0.94
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 5HDN · PDBe 5HDN · UniProt Q00613
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