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Crystal structure of parn nuclease domain

Analyse Crystal structure of parn nuclease domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2A1R
Type: protein + RNA
Length: 598 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*AP*AP*A)-3'; POLY(A)-specific ribonuclease parn
EC: 3.1.13.4
UniProt: O95453
Pockets: 9 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	5'-R(APAP*A)-3'	rna	3	—	—
A	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	300	41% helix, 17% strand	O95453
B	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	292	39% helix, 18% strand	O95453

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	297	0.58	0.77	34	empty
2	235	0.57	0.78	32	empty
3	267	0.54	0.76	31	empty
4	186	0.53	0.78	28	empty
5	105	0.40	0.76	15	empty

Interfaces

5 interfaces between chains.

A–B · 1206 Å² buried · 32 hydrogen bonds · protein-protein
C–A · 517 Å² buried · 10 hydrogen bonds · protein-nucleic
D–B · 517 Å² buried · 9 hydrogen bonds · protein-nucleic
C–B · 52 Å² buried · 1 hydrogen bond · protein-nucleic
D–A · 35 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2A1R · Crystal structure of PARN nuclease domain · the same entry in another collection · chain C against C, TM-score 1.00
O95453 · AlphaFold monomer V2.0 prediction for POLY(A)-specific ribonuclease parn (O95453) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O95453
Elsewhere: RCSB PDB 2A1R · PDBe 2A1R · UniProt O95453

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