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Crystal Structure of phi29 pRNA 3WJ Core

Analyse Crystal Structure of phi29 pRNA 3WJ Core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KZ2
Type: RNA
Length: 54 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.05
Molecule: phi29 pRNA 3WJ core RNA 18 mer; phi29 pRNA 3WJ core RNA 20 mer; phi29 pRNA 3WJ core RNA…
Ligands: MN
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · resolution 3.05 · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	phi29 pRNA 3WJ core RNA 18 mer	rna	18	—	—
B	phi29 pRNA 3WJ core RNA 20 mer	rna	20	—	—
C	phi29 pRNA 3WJ core RNA 16 mer	rna	16	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 3 copies · chains A, C, 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	477	0.57	0.74	22	empty
2	169	0.37	0.72	19	empty

Interfaces

3 interfaces between chains.

A–B · 653 Å² buried · 60 hydrogen bonds · nucleic-nucleic
B–C · 433 Å² buried · 40 hydrogen bonds · nucleic-nucleic
A–C · 408 Å² buried · 38 hydrogen bonds · nucleic-nucleic

Compared structures

4KZ2 · Crystal structure of PHI29 prna 3WJ core · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4KZ2 · PDBe 4KZ2

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