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Pistol ribozyme transition-state analog vanadate

Analyse Pistol ribozyme transition-state analog vanadate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UF1
Type: RNA
Length: 130 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (50-mer); RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(GVA)*UP*CP*CP*AP*A)- 3')
Ligands: MN
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA (50-mer)	rna	50	—	—
B, D	RNA (5'-R(UPCPUPGPCPUPCPUPCP(GVA)UPCPCPAP*A)- 3')	rna	15	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 17 copies · chains A, B, C, D

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	1119	0.78	0.81	66	MN
2	251	0.48	0.74	17	MN
3	236	0.46	0.74	17	MN
4	116	0.39	0.76	15	MN

Interfaces

3 interfaces between chains.

A–B · 904 Å² buried · 72 hydrogen bonds · nucleic-nucleic
C–D · 897 Å² buried · 71 hydrogen bonds · nucleic-nucleic
A–C · 305 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

6UF1 · Pistol ribozyme transition-state analog vanadate · 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 6UF1 · PDBe 6UF1

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