Research workbench
Human HSF2 DNA binding domain in complex with 3-site hse DNA at 2.1 ångströms resolution
Analyse Human HSF2 DNA binding domain in complex with 3-site hse DNA at 2.1 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D8L
- Type
- protein + DNA
- Length
- 475 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3'); Heat shock factor…
- UniProt
- Q03933
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | DNA (5'- D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3') | dna | 17 | — | — |
| B, H | Heat shock factor protein 2 | protein | 106 | 40% helix, 11% strand | Q03933 |
| C, E | DNA (5'- D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3') | dna | 17 | — | — |
| D | Heat shock factor protein 2 | protein | 97 | 43% helix, 12% strand | Q03933 |
| F | Heat shock factor protein 2 | protein | 98 | 42% helix, 12% strand | Q03933 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.86 | 0.87 | 86 | empty |
| 2 | 498 | 0.82 | 0.89 | 45 | empty |
| 3 | 170 | 0.51 | 0.78 | 28 | empty |
| 4 | 106 | 0.42 | 0.78 | 21 | empty |
| 5 | 165 | 0.41 | 0.74 | 24 | empty |
Interfaces
22 interfaces between chains.
- A–C · 763 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- E–G · 762 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–C · 449 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 447 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 420 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- Q03933 · AlphaFold monomer V2.0 prediction for heat shock factor protein 2 (Q03933) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 5D8L · PDBe 5D8L · UniProt Q03933
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