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Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-MN2+

Analyse Two active site divalent ion in the crystal structure of the hammerhead… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EAQ
Type: RNA
Length: 68 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (48-mer); RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)…
Ligands: MN
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (48-mer)	rna	48	—	—
B	RNA (5'-R(GPGPGPCPGPU(CVC) UPGPGPGPCPAPGPUPAPCPCPCPA)-3')	rna	20	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 6 copies · chains A, B

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

Pockets

4 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	288	0.52	0.75	21	MN
2	114	0.33	0.73	12	empty
3	94	0.30	0.73	14	MN
4	51	0.24	0.73	6	empty

Interfaces

1 interface between chains.

A–B · 952 Å² buried · 61 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5EAQ · Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5EAQ · PDBe 5EAQ

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