MolNFT v1 · #9140 · DNA + RNA

Three-dimensional structure of a hammerhead ribozyme

1HMH · Hammerhead ribozyme-RNA strand: “Three-dimensional structure of a hammerhead ribozyme”. X-ray diffraction, 3 pockets (best druggability 0.44). MolNFT v1 #9140 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1HMH
Type: DNA + RNA
Length: 141 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hammerhead ribozyme-RNA strand; Hammerhead ribozyme-DNA strand
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Hammerhead ribozyme-RNA strand	rna	34	—	—
B, D, F	Hammerhead ribozyme-DNA strand	dna	13	—	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.44	0.74	16	empty
2	118	0.35	0.74	11	empty
3	96	0.30	0.72	9	empty

Interfaces

5 interfaces between chains.

E–F · 832 Å² buried · 85 hydrogen bonds · nucleic-nucleic
C–D · 815 Å² buried · 78 hydrogen bonds · nucleic-nucleic
A–B · 811 Å² buried · 95 hydrogen bonds · nucleic-nucleic
A–E · 458 Å² buried · 12 hydrogen bonds · nucleic-nucleic
A–C · 427 Å² buried · 16 hydrogen bonds · nucleic-nucleic

Compared structures

1HMH · Three-dimensional structure of a hammerhead ribozyme · the same entry in another collection · chain F against F, 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 1HMH · PDBe 1HMH

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