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Structure of a four-way junction in an inverted repeat sequence.

Analyse Structure of a four-way junction in an inverted repeat sequence. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DCW
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
Ligands: NA
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

NA · Sodium ion · metal · chains B, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.45	0.73	20	empty
2	208	0.42	0.73	19	empty

Interfaces

6 interfaces between chains.

C–D · 310 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–B · 308 Å² buried · 30 hydrogen bonds · nucleic-nucleic
B–C · 221 Å² buried · 23 hydrogen bonds · nucleic-nucleic
A–D · 220 Å² buried · 22 hydrogen bonds · nucleic-nucleic
B–D · 213 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

1DCW · Structure of a four-way junction in an inverted repeat sequence. · 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 1DCW · PDBe 1DCW

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