Research workbench

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

Analyse Crystal structure of a hairpin ribozyme in the catalytically-active conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M5K
Type: protein + RNA
Length: 410 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA inhibitor substrate; RNA hairpin ribozyme; Protein (U1 small nuclear…
UniProt: P09012
Ligands: CA, CL
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	RNA inhibitor substrate	rna	21	—	—
B, E	RNA hairpin ribozyme	rna	92	—	—
C, F	Protein (U1 small nuclear ribonucleoprotein a)	protein	92	33% helix, 26% strand	P09012

Ligands and binding sites

CA · Calcium ion · metal · 33 copies · chains A, B, D, E, F
CL · Chloride ion · ion · 2 copies · chains F

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.69	0.75	48	CA
2	816	0.67	0.75	48	CA, CL
3	632	0.66	0.76	31	CA
4	738	0.65	0.75	41	CA
5	435	0.55	0.74	24	empty

Interfaces

5 interfaces between chains.

D–E · 1512 Å² buried · 94 hydrogen bonds · nucleic-nucleic
A–B · 1426 Å² buried · 101 hydrogen bonds · nucleic-nucleic
B–C · 931 Å² buried · 28 hydrogen bonds · protein-nucleic
E–F · 899 Å² buried · 33 hydrogen bonds · protein-nucleic
C–F · 224 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

1M5K · Crystal structure of a hairpin ribozyme in the catalytically-active conformation · 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
Every structure of UniProt P09012
Elsewhere: RCSB PDB 1M5K · PDBe 1M5K · UniProt P09012

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.