MolNFT v1 · #38828 · protein + DNA
Structure of a HAP1-18/DNA complex reveals that PROTEIN/DNA interactions can have direct allosteric effects on transcriptional activation
2HAP · DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*…: “Structure of a HAP1-18/DNA complex reveals that PROTEIN/DNA interactions can have direct allosteric effects…”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best…
- PDB
- 2HAP
- Type
- protein + DNA
- Length
- 191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3'); DNA (5'…
- UniProt
- P12351
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3') | dna | 20 | — | — |
| B | DNA (5'- D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3') | dna | 20 | — | — |
| C | Protein (heme activator protein) | protein | 76 | 55% helix, 0% strand | P12351 |
| D | Protein (heme activator protein) | protein | 75 | 55% helix, 0% strand | P12351 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.48 | 0.81 | 21 | empty |
| 2 | 131 | 0.46 | 0.78 | 19 | empty |
| 3 | 73 | 0.33 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1154 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 914 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- B–D · 580 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 460 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 443 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 2HAP · Structure of a HAP1-18/DNA complex reveals that PROTEIN/DNA interactions can have direct… · 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 2HAP · PDBe 2HAP · UniProt P12351
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