Research workbench

Structure of an S. pombe APTX/DNA/AMP/ZN complex

Analyse Structure of an S. pombe APTX/DNA/AMP/ZN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SZQ
Type: protein + DNA
Length: 212 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aprataxin-like protein; 5'-D(*CP*CP*CP*TP*G)-3'…
EC: 3.-.-.-
UniProt: O74859
Ligands: AMP, ZN
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aprataxin-like protein (EC 3.-.-.-)	protein	199	43% helix, 16% strand	O74859
B	5'-D(CPCPCPTP*G)-3'	dna	5	—	—
C	5'-D(TPAPTPCPGPGPAPAPTPCPAPGPGPG)-3'	dna	8	—	—

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A, B
ZN · Zinc ion · metal · chains A
BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	530	0.68	0.78	43	AMP, BME
2	85	0.39	0.77	12	empty

Interfaces

3 interfaces between chains.

A–B · 272 Å² buried · 3 hydrogen bonds · protein-nucleic
B–C · 244 Å² buried · 24 hydrogen bonds · nucleic-nucleic
A–C · 236 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

3SZQ · Structure of an S. pombe APTX/DNA/AMP/Zn complex · the same entry in another collection · chain A against A, 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 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 O74859
Elsewhere: RCSB PDB 3SZQ · PDBe 3SZQ · UniProt O74859

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.