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Crystal structure of an a-DNA dodecamer containing the gggccc motif

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

PDB: 5MVP
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA
Ligands: K
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA	dna	12	—	—

Ligands and binding sites

K · Potassium ion · metal · 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	285	0.48	0.73	16	K

Interfaces

1 interface between chains.

A–B · 591 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Compared structures

5MVP · Crystal structure of an A-DNA dodecamer containing the GGGCCC motif · 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 5MVP · PDBe 5MVP

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