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Crystal structure of the a-DNA hexamer GGCGM5CC

Analyse Crystal structure of the a-DNA hexamer GGCGM5CC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1F6E
Type: DNA
Length: 34 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*GP*CP*GP*(5CM)P*C)-3')
Pockets: 1 · best druggability 0.25

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(GPGPCPGP(5CM)PC)-3')	dna	6	—	—
E	DNA (5'-D(GPGPCPGP(5CM)PC)-3')	dna	5	—	—
F	DNA (5'-D(GPGPCPGP(5CM)PC)-3')	dna	5	—	—

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	53	0.25	0.73	12	empty

Interfaces

9 interfaces between chains.

A–B · 296 Å² buried · 22 hydrogen bonds · nucleic-nucleic
C–D · 292 Å² buried · 24 hydrogen bonds · nucleic-nucleic
E–F · 245 Å² buried · 22 hydrogen bonds · nucleic-nucleic
C–E · 113 Å² buried · 1 hydrogen bond · nucleic-nucleic
D–E · 112 Å² buried · 3 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

1F6E · Crystal structure of the a-DNA hexamer GGCGM5CC · 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 1F6E · PDBe 1F6E

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