MolNFT v1 · #5503 · DNA + RNA

Solution structure of a hna-RNA hybrid

1EJZ · RNA (5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'): “Solution structure of a hna-RNA hybrid”. Solution nmr, 1 ligand (PDI), 1 pocket (best druggability 0.25). MolNFT v1 #5503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1EJZ
Type: DNA + RNA
Length: 16 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'); DNA (5'-H(*(6HG)P*(6HC)P*(6HG)P*(6HT)P*(6HA)P*(6HG…
Ligands: PDI
Pockets: 1 · best druggability 0.25

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'-R(CPGPCPUPAPCPGPC)-3')	rna	8	—	—
B	DNA (5'-H((6HG)P(6HC)P(6HG)P(6HT)P(6HA)P(6HG)P(6HC) P(6HG))-3')	dna	8	—	—

Ligands and binding sites

PDI · Phosphoric acid mono-(3-hydroxy-propyl) ester · ligand · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.25	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 400 Å² buried · 60 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 8 modified, 1 covalent (nucleotide modification, covalent ligand).

Compared structures

1EJZ · Solution structure of a hna-RNA hybrid · 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 1EJZ · PDBe 1EJZ

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