MolNFT v1 · #100979 · protein + DNA
Human aprataxin (aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and zn - product complex
4NDI: “Human aprataxin (aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and zn - product complex”. X-ray diffraction, 4 ligands (AMP, ZN, K), 6 pockets (best druggability 0.75). MolNFT v1 #100979 on GenesisL1: 3D structure, binding sites…
- PDB
- 4NDI
- Type
- protein + DNA
- Length
- 400 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aprataxin; 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'…
- UniProt
- Q7Z2E3
- Ligands
- AMP, ZN, K, NA
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aprataxin | protein | 180 | 37% helix, 17% strand | Q7Z2E3 |
| D, G | 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3' | dna | 10 | — | — |
| E, H | 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3' | dna | 10 | — | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, D, B, G
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains D, E, G, H
- NA · Sodium ion · metal · chains A, D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, D, B, G
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.75 | 0.80 | 83 | AMP |
| 2 | 152 | 0.68 | 0.88 | 26 | AMP |
| 3 | 616 | 0.67 | 0.77 | 46 | NA, K |
| 4 | 475 | 0.60 | 0.75 | 31 | empty |
| 5 | 75 | 0.47 | 0.82 | 18 | empty |
Interfaces
9 interfaces between chains.
- G–H · 410 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- D–E · 391 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–B · 389 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 371 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–G · 339 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4NDI · Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q7Z2E3 · AlphaFold monomer V2.0 prediction for aprataxin (Q7Z2E3) · a predicted model of the same protein · chain B 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 Q7Z2E3
- Elsewhere: RCSB PDB 4NDI · PDBe 4NDI · UniProt Q7Z2E3
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