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Crystal structure of a group I ribozyme domain: principles of RNA packing

Analyse Crystal structure of a group I ribozyme domain: principles of RNA packing in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GID
Type: RNA
Length: 316 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P4-P6 RNA ribozyme domain
Ligands: NCO, MG
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	P4-P6 RNA ribozyme domain	rna	158	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 4 copies · chains A, B
MG · Magnesium ion · metal · 24 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	433	0.75	0.86	43	MG
2	327	0.71	0.85	21	empty
3	276	0.70	0.86	27	MG
4	522	0.68	0.80	38	MG, NCO
5	281	0.68	0.84	21	empty

Interfaces

1 interface between chains.

A–B · 973 Å² buried · 34 hydrogen bonds · nucleic-nucleic

Compared structures

1GID · Crystal structure of a group I ribozyme domain: principles of RNA packing · 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 1GID · PDBe 1GID

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