Research workbench
Crystal structure of aprataxin ortholog HNT3 in complex with DNA and AMP
Analyse Crystal structure of aprataxin ortholog HNT3 in complex with DNA and AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SPL
- Type
- protein + DNA
- Length
- 856 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aprataxin-like protein; DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)- 3'); DNA…
- UniProt
- O74859
- Ligands
- AMP, ZN, SO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aprataxin-like protein | protein | 200 | 43% helix, 16% strand | O74859 |
| E, G | DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)- 3') | dna | 14 | — | — |
| F, H | DNA (5'- D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3') | dna | 14 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 16 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.83 | 0.84 | 89 | SO4 |
| 2 | 991 | 0.83 | 0.84 | 88 | SO4 |
| 3 | 142 | 0.69 | 0.89 | 24 | AMP |
| 4 | 158 | 0.69 | 0.88 | 28 | AMP |
| 5 | 141 | 0.68 | 0.89 | 25 | AMP |
Interfaces
12 interfaces between chains.
- E–F · 559 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- G–H · 558 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- B–C · 553 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 482 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3SPL · Crystal structure of aprataxin ortholog Hnt3 in complex with DNA and AMP · the same entry in another collection · chain C against C, TM-score 1.00
- O74859 · AlphaFold monomer V2.0 prediction for aprataxin-like protein (O74859) · a predicted model of the same protein · 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 O74859
- Elsewhere: RCSB PDB 3SPL · PDBe 3SPL · UniProt O74859
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