MolNFT v1 · #9445 · protein + DNA
Structure of a HAP1/DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein
1HWT · DNA (5'- D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*…: “Structure of a HAP1/DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein”. X-ray diffraction, 1 ligand (ZN), 15 pockets (best druggability…
- PDB
- 1HWT
- Type
- protein + DNA
- Length
- 367 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP *C)-3'); DNA (5'…
- UniProt
- P12351
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA (5'- D(*GP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP *C)-3') | dna | 20 | — | — |
| B, F | DNA (5'- D(*GP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP *C)-3') | dna | 20 | — | — |
| C, G | Protein (heme activator protein) | protein | 70 | 59% helix, 0% strand | P12351 |
| D | Protein (heme activator protein) | protein | 74 | 51% helix, 0% strand | P12351 |
| H | Protein (heme activator protein) | protein | 73 | 55% helix, 0% strand | P12351 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains C, D, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.68 | 0.88 | 26 | empty |
| 2 | 158 | 0.67 | 0.87 | 28 | empty |
| 3 | 159 | 0.57 | 0.82 | 23 | empty |
| 4 | 199 | 0.56 | 0.79 | 23 | empty |
| 5 | 246 | 0.51 | 0.75 | 36 | empty |
Interfaces
21 interfaces between chains.
- C–D · 1174 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1167 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- E–F · 908 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- D–H · 899 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1HWT · Structure of a HAP1/DNA complex reveals dramatically asymmetric DNA binding by a… · the same entry in another collection · chain A against A, TM-score 1.00
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 P12351
- Elsewhere: RCSB PDB 1HWT · PDBe 1HWT · UniProt P12351
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