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Crystal structure of the zalpha Z-DNA complex

Analyse Crystal structure of the zalpha Z-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QBJ
Type: protein + DNA
Length: 212 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3'); Protein (double-stranded RNA specific adenosine…
UniProt: P55265
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 4 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F	DNA (5'-D(TPCPGPCPGPCP*G)-3')	dna	6	—	—
A	Protein (double-stranded RNA specific adenosine deaminase (ADAR1))	protein	65	57% helix, 14% strand	P55265
B	Protein (double-stranded RNA specific adenosine deaminase (ADAR1))	protein	63	54% helix, 14% strand	P55265
C	Protein (double-stranded RNA specific adenosine deaminase (ADAR1))	protein	66	58% helix, 12% strand	P55265

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	234	0.50	0.75	19	empty
2	191	0.49	0.77	24	empty

Interfaces

7 interfaces between chains.

F–C · 428 Å² buried · 7 hydrogen bonds · protein-nucleic
E–B · 427 Å² buried · 10 hydrogen bonds · protein-nucleic
D–A · 404 Å² buried · 8 hydrogen bonds · protein-nucleic
D–E · 326 Å² buried · 28 hydrogen bonds · nucleic-nucleic
B–C · 184 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1QBJ · Crystal structure of the zalpha Z-DNA complex · the same entry in another collection · chain C against C, TM-score 1.00
P55265 · AlphaFold monomer V2.0 prediction for double-stranded RNA-specific adenosine deaminase… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P55265
Elsewhere: RCSB PDB 1QBJ · PDBe 1QBJ · UniProt P55265

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