Research workbench

Crystal structure of D(G4C2)2-ba in C2221 space group

Analyse Crystal structure of D(G4C2)2-ba in C2221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ECF
Type: DNA
Length: 72 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
Ligands: BA
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA (5'-D(GPGPGPGPCPCPGPGPGPGPCPC)-3')	dna	12	—	—

Ligands and binding sites

BA · Barium ion · metal · 7 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.59	0.86	15	BA
2	177	0.50	0.78	17	empty

Interfaces

10 interfaces between chains.

A–C · 433 Å² buried · 8 hydrogen bonds · nucleic-nucleic
C–D · 368 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–B · 349 Å² buried · 30 hydrogen bonds · nucleic-nucleic
E–F · 346 Å² buried · 30 hydrogen bonds · nucleic-nucleic
B–E · 295 Å² buried · 11 hydrogen bonds · nucleic-nucleic

Compared structures

7ECF · Crystal Structure of d(G4C2)2-Ba in C2221 space group · 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 7ECF · PDBe 7ECF

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.