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Holliday junction tcggtaccga with na and ca binding sites.

Analyse Holliday junction tcggtaccga with na and ca binding sites. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L4J
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
Ligands: CA, NA
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, D, B, C
NA · Sodium ion · metal · 2 copies · chains C, 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	249	0.46	0.73	20	NA
2	250	0.45	0.73	21	empty

Interfaces

6 interfaces between chains.

C–D · 308 Å² buried · 23 hydrogen bonds · nucleic-nucleic
A–B · 304 Å² buried · 25 hydrogen bonds · nucleic-nucleic
A–D · 224 Å² buried · 17 hydrogen bonds · nucleic-nucleic
B–D · 223 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 212 Å² buried · 16 hydrogen bonds · nucleic-nucleic

Compared structures

1L4J · Holliday Junction TCGGTACCGA with Na and Ca Binding Sites. · 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 1L4J · PDBe 1L4J

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