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Crystal structure of a vitamin B12 binding RNA aptamer with ligand at 2.3 a

Analyse Crystal structure of a vitamin B12 binding RNA aptamer with ligand at 2.3 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ET4
Type: RNA
Length: 175 nucleotides
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA aptamer, 35-mer
Ligands: CNC
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	RNA aptamer, 35-mer	rna	35	—	—

Ligands and binding sites

CNC · Cyanocobalamin · ligand · 5 copies · chains A, B, C, E, D

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

Pockets

8 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	928	0.66	0.74	50	empty
2	685	0.62	0.74	31	empty
3	168	0.47	0.77	16	empty
4	221	0.45	0.74	20	empty
5	110	0.38	0.76	15	empty

Interfaces

4 interfaces between chains.

C–D · 677 Å² buried · 22 hydrogen bonds · nucleic-nucleic
A–B · 671 Å² buried · 26 hydrogen bonds · nucleic-nucleic
C–E · 307 Å² buried · 9 hydrogen bonds · nucleic-nucleic
D–E · 63 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

1ET4 · Crystal structure of a vitamin B12 binding RNA aptamer with ligand at 2.3 a · 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 1ET4 · PDBe 1ET4

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