MolNFT v1 · #160514 · RNA

Co-crystal structure of the geobacillus kaustophilus glyq T-box riboswitch discriminator domain in complex with tRNA-gly

6PMO: “Co-crystal structure of the geobacillus kaustophilus glyq T-box riboswitch discriminator domain in complex…”. X-ray diffraction, 2 ligands (IR, MG), 4 pockets (best druggability 0.73). MolNFT v1 #160514 on GenesisL1: 3D structure…

PDB: 6PMO
Type: RNA
Length: 130 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-gly; T-box riboswitch discriminator
Ligands: IR, MG
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	TRNA-gly	rna	70	—	—
A	T-box riboswitch discriminator	rna	60	—	—

Ligands and binding sites

IR · Iridium ion · metal · 13 copies · chains B, A
MG · Magnesium ion · metal · 4 copies · chains B, A

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	1071	0.73	0.77	57	MG, IR
2	384	0.61	0.78	22	IR
3	293	0.54	0.76	19	IR
4	168	0.38	0.72	15	empty

Interfaces

1 interface between chains.

B–A · 496 Å² buried · 29 hydrogen bonds · nucleic-nucleic

Compared structures

6PMO · Co-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator… · 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
Elsewhere: RCSB PDB 6PMO · PDBe 6PMO

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