MolNFT v1 · #181217 · RNA

RNA dodecamer containing a gna a residue

7LO9 · Chains: A,B,C,D: “RNA dodecamer containing a gna a residue”. X-ray diffraction, 1 ligand (ZAD), 2 pockets (best druggability 0.42). MolNFT v1 #181217 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7LO9
Type: RNA
Length: 44 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chains: A,B,C,D
Ligands: ZAD
Pockets: 2 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Chains: A,B,C,D	rna	11	—	—

Ligands and binding sites

ZAD · (S)-1'-(2',3'-dihydroxypropyl)-adenine · ligand · 4 copies · 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	187	0.42	0.74	18	ZAD
2	170	0.38	0.72	14	ZAD

Interfaces

5 interfaces between chains.

A–B · 599 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–D · 596 Å² buried · 48 hydrogen bonds · nucleic-nucleic
B–C · 111 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 101 Å² buried · 4 hydrogen bonds · nucleic-nucleic
B–D · 82 Å² buried · 1 hydrogen bond · nucleic-nucleic

Modifications

Observed in the structure: 8 covalent, 4 modified (covalent ligand, nucleotide modification).

Compared structures

7LO9 · RNA dodecamer containing a GNA A residue · 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 7LO9 · PDBe 7LO9

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