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Crystal structure of the ragath-18 K-turn

Analyse Crystal structure of the ragath-18 K-turn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EAG
Type: RNA
Length: 95 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D, E, F	RNA (5'- R(GPUPCPUPAPUPGPAPAPGPGPCPUPGPGPAPGPAP*C)-3')	rna	19	—	—
A	RNA (5'- R(GPUPCPUPAPUPGPAPAPGPGPCPUPGPGPAPGPAP*C)-3')	rna	11	—	—
B	RNA (5'- R(GPUPCPUPAPUPGPAPAPGPGPCPUPGPGPAPGPAP*C)-3')	rna	8	—	—

Pockets

2 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	493	0.59	0.75	27	empty
2	368	0.52	0.74	24	empty

Interfaces

7 interfaces between chains.

E–F · 1271 Å² buried · 107 hydrogen bonds · nucleic-nucleic
C–D · 1270 Å² buried · 114 hydrogen bonds · nucleic-nucleic
A–B · 641 Å² buried · 59 hydrogen bonds · nucleic-nucleic
D–E · 101 Å² buried · 5 hydrogen bonds · nucleic-nucleic
C–A · 84 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Compared structures

7EAG · Crystal structure of the RAGATH-18 k-turn · the same entry in another collection · chain C against C, 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 7EAG · PDBe 7EAG

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