MolNFT v1 · #118952 · DNA

Extensive amphimorphism in DNA: three stable conformations for the decadeoxynucleotide D(GCATGCATGC)

5FHJ · DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3'): “Extensive amphimorphism in DNA: three stable conformations for the decadeoxynucleotide D(GCATGCATGC)”. X-ray diffraction, 1 ligand (CO), 1 pocket (best druggability 0.29). MolNFT v1…

PDB: 5FHJ
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
Ligands: CO
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

CO · Cobalt (II) ion · metal · 7 copies · chains A, B, C, D

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	79	0.29	0.73	13	empty

Interfaces

5 interfaces between chains.

C–D · 514 Å² buried · 46 hydrogen bonds · nucleic-nucleic
A–B · 341 Å² buried · 20 hydrogen bonds · nucleic-nucleic
A–C · 135 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 89 Å² buried · 2 hydrogen bonds · nucleic-nucleic
B–D · 89 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

5FHJ · Extensive amphimorphism in DNA: Three stable conformations for the decadeoxynucleotide… · 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 5FHJ · PDBe 5FHJ

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