MolNFT v1 · #36852 · DNA

Crystal structure analysis of the a-DNA decamer gcgt-2'OMEA-au-acgc, with incorporated 2'-O-methylated-adenosine (2'OMEA) and arabino- uridine (au)

2FIJ · 5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3': “Crystal structure analysis of the a-DNA decamer gcgt-2'OMEA-au-acgc, with incorporated…”. X-ray diffraction, 2 ligands (NCO, CL), 1 pocket (best druggability 0.39). MolNFT v1 #36852…

PDB: 2FIJ
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3'
Ligands: NCO, CL
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(GPCPGPTP(A2M)P(UAR)PAPCPGPC)-3'	dna	10	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B
CL · Chloride ion · ion · chains A, 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	152	0.39	0.73	13	CL, NCO

Interfaces

1 interface between chains.

A–B · 451 Å² buried · 42 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

2FIJ · Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated… · 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 2FIJ · PDBe 2FIJ

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