MolNFT v1 · #63984 · DNA

Crystal structure of D(CACGCG).D(CGCGTG) with 10MM MNCL2

3FQ5 · 5'-D(*CP*AP*CP*GP*CP*G)-3': “Crystal structure of D(CACGCG).D(CGCGTG) with 10MM MNCL2”. X-ray diffraction, 1 ligand (MN). MolNFT v1 #63984 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3FQ5
Type: DNA
Length: 24 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*AP*CP*GP*CP*G)-3'; 5'-D(*CP*GP*CP*GP*TP*G)-3'
Ligands: MN

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	5'-D(CPAPCPGPCPG)-3'	dna	6	—	—
B, D	5'-D(CPGPCPGPTPG)-3'	dna	6	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, D

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

Interfaces

5 interfaces between chains.

C–D · 335 Å² buried · 31 hydrogen bonds · nucleic-nucleic
A–B · 329 Å² buried · 27 hydrogen bonds · nucleic-nucleic
B–D · 131 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–D · 46 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–C · 11 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

3FQ5 · Crystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2 · 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 3FQ5 · PDBe 3FQ5

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