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Crystal structure of D(G4C2)2-ba in F222 space group

Analyse Crystal structure of D(G4C2)2-ba in F222 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ECG
Type: DNA
Length: 33 nucleotides
Chains: 3
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: 1 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(GPGPGPGPCPCPGPGPGPGPCPC)-3')	dna	12	—	—
B	DNA (5'-D(GPGPGPGPCPCPGPGPGPGPCPC)-3')	dna	11	—	—
C	DNA (5'-D(GPGPGPGPCPCPGPGPGPGPCPC)-3')	dna	10	—	—

Ligands and binding sites

BA · Barium ion · metal · 5 copies · chains A, C, 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	149	0.41	0.75	16	BA

Interfaces

3 interfaces between chains.

B–C · 352 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–C · 288 Å² buried · 8 hydrogen bonds · nucleic-nucleic
A–B · 114 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Compared structures

7ECG · Crystal Structure of d(G4C2)2-Ba in F222 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 7ECG · PDBe 7ECG

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