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Racemic crystal structures of pribnow box consensus promoter sequence (pbca)

Analyse Racemic crystal structures of pribnow box consensus promoter sequence (pbca) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EZF
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pribnow box template strand; Complementary strand
Ligands: CA
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pribnow box template strand	dna	12	—	—
B	Complementary strand	dna	12	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B, A

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	74	0.30	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 552 Å² buried · 52 hydrogen bonds · nucleic-nucleic

Compared structures

5EZF · Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca) · 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 5EZF · PDBe 5EZF

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