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A second look at the hdv ribozyme structure and dynamics.

Analyse A second look at the hdv ribozyme structure and dynamics. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PRF
Type: protein + RNA
Length: 169 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatitis delta virus ribozyme; U1 small nuclear ribonucleoprotein a
UniProt: P09012
Ligands: SR
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Hepatitis delta virus ribozyme	rna	74	—	—
A	U1 small nuclear ribonucleoprotein a	protein	95	32% helix, 25% strand	P09012

Ligands and binding sites

SR · Strontium ion · metal · 2 copies · chains B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.66	0.77	29	empty
2	340	0.58	0.77	23	SR
3	219	0.43	0.73	17	empty
4	93	0.37	0.76	19	empty
5	77	0.33	0.76	12	SR

Interfaces

1 interface between chains.

B–A · 958 Å² buried · 36 hydrogen bonds · protein-nucleic

Compared structures

4PRF · A Second Look at the HDV Ribozyme Structure and Dynamics. · the same entry in another collection · chain B against B, 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 4PRF · PDBe 4PRF · UniProt P09012

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