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Structure of yeast POLY(A) polymerase with ATP and OLIGO(A)

Analyse Structure of yeast POLY(A) polymerase with ATP and OLIGO(A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Q66
Type: protein + RNA
Length: 524 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(P*AP*AP*AP*AP*A)-3'; POLY(A) polymerase
EC: 2.7.7.19
UniProt: P29468
Ligands: ATP, MG
Pockets: 3 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	5'-R(PAPAPAPAP*A)-3'	rna	5	—	—
A	POLY(A) polymerase (EC 2.7.7.19)	protein	519	45% helix, 17% strand	P29468

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains X, A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 17 copies · chains X, A

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

Pockets

3 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	914	0.81	0.83	91	MG, ATP, EDO
2	144	0.46	0.77	22	EDO
3	68	0.34	0.77	15	empty

Interfaces

1 interface between chains.

X–A · 914 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

2Q66 · Structure of Yeast Poly(A) Polymerase with ATP and oligo(A) · the same entry in another collection · chain X against X, TM-score 1.00
P29468 · AlphaFold monomer V2.0 prediction for POLY(A) polymerase (P29468) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P29468
Elsewhere: RCSB PDB 2Q66 · PDBe 2Q66 · UniProt P29468

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