MolNFT v1 · #78977 · protein + DNA
Crystal structure of aprataxin ortholog HNT3 in complex with DNA and AMP
3SPL · Aprataxin-like protein: “Crystal structure of aprataxin ortholog HNT3 in complex with DNA and AMP”. X-ray diffraction, 3 ligands (AMP, ZN, SO4), 14 pockets (best druggability 0.83). MolNFT v1 #78977 on GenesisL1: 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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