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Crystal structure of native parn nuclease domain

Analyse Crystal structure of native 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: 2A1S
Type: protein
Length: 1,566 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POLY(A)-specific ribonuclease parn
EC: 3.1.13.4
UniProt: O95453
Pockets: 20 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	391	40% helix, 17% strand	O95453
B	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	390	43% helix, 16% strand	O95453
C	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	393	42% helix, 19% strand	O95453
D	POLY(A)-specific ribonuclease parn (EC 3.1.13.4)	protein	392	40% helix, 18% strand	O95453

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.64	0.77	36	empty
2	421	0.61	0.76	48	empty
3	324	0.56	0.76	38	empty
4	233	0.56	0.78	31	empty
5	230	0.53	0.77	31	empty

Interfaces

3 interfaces between chains.

A–C · 1151 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 1131 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 1131 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2A1S · Crystal structure of native PARN nuclease domain · the same entry in another collection · chain D against D, 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 C 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 O95453
Elsewhere: RCSB PDB 2A1S · PDBe 2A1S · UniProt O95453

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