MolNFT v1 · #38517 · RNA

Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme

2H0S · Glms ribozyme deoxy RNA inhibitor: “Pre-cleavage state of the thermoanaerobacter tengcongensis glms ribozyme”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.76). MolNFT v1 #38517 on GenesisL1: 3D structure…

PDB: 2H0S
Type: RNA
Length: 145 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glms ribozyme deoxy RNA inhibitor; Glms ribozyme RNA
Ligands: MG
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glms ribozyme deoxy RNA inhibitor	rna	22	—	—
B	Glms ribozyme RNA	rna	123	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1113	0.76	0.79	57	MG
2	335	0.60	0.78	22	empty
3	433	0.56	0.74	28	MG
4	248	0.45	0.73	23	empty

Interfaces

1 interface between chains.

A–B · 1530 Å² buried · 101 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2H0S · Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme · 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 2H0S · PDBe 2H0S

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