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1.66 a structure of a-duplex with bulged adenosine, spermine form

Analyse 1.66 a structure of a-duplex with bulged adenosine, spermine form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I2Y
Type: RNA
Length: 66 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (5'-R(*GP*CP*G)-D(P*AP*TP*AP*T)- R(P*AP*CP*GP*U)-3')
Ligands: SPM
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA/RNA (5'-R(GPCPG)-D(PAPTPAPT)- R(PAPCPGP*U)-3')	rna	11	—	—

Ligands and binding sites

SPM · Spermine · ligand · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.32	0.72	17	empty
2	62	0.24	0.72	12	empty

Interfaces

9 interfaces between chains.

C–D · 474 Å² buried · 43 hydrogen bonds · nucleic-nucleic
A–B · 473 Å² buried · 34 hydrogen bonds · nucleic-nucleic
E–F · 468 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–E · 89 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–C · 85 Å² buried · 3 hydrogen bonds · nucleic-nucleic

Compared structures

1I2Y · 1.66 a structure of a-duplex with bulged adenosine, spermine form · 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 1I2Y · PDBe 1I2Y

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