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Crystal structure of the ANA:RNA decamer suffering from lattice translocation defects

Analyse Crystal structure of the ANA:RNA decamer suffering from lattice translocation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OK4
Type: RNA
Length: 300 nucleotides
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ana; RNA
Ligands: PO4

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O, Q, S, U, W, Y, 1, 3	Ana	rna	10	—	—
B, D, F, H, J, L, N, P, R, T, V, X, Z, 2, 4	RNA	rna	10	—	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 15 copies · chains A, C, K, E, G, I, Q, M, O, W, S, U, 3, Y, 1

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

Interfaces

107 interfaces between chains.

G–O · 995 Å² buried · 355 hydrogen bonds · nucleic-nucleic
A–I · 991 Å² buried · 363 hydrogen bonds · nucleic-nucleic
S–1 · 991 Å² buried · 374 hydrogen bonds · nucleic-nucleic
M–U · 989 Å² buried · 357 hydrogen bonds · nucleic-nucleic
U–3 · 989 Å² buried · 354 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 150 modified (nucleotide modification).

Compared structures

3OK4 · Crystal structure of the ANA:RNA decamer suffering from lattice translocation defects · 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 3OK4 · PDBe 3OK4

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