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Crystal structure of D(CGCGAATXCGCG) where X is 5-(N- AMINOHEXYL)CARBAMOYL-2'-deoxyuridine

Analyse Crystal structure of D(CGCGAATXCGCG) where X is 5-(N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DPB
Type: DNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3')
Ligands: CMY, K
Pockets: 1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'- D(DCPDGPDCPDGPDAPDAPDTPDUPDCPDGPDCPDG)-3')	dna	12	—	—

Ligands and binding sites

CMY · (6-aminohexyl)carbamic acid · ligand · 2 copies · chains A, B
K · Potassium ion · metal · chains A, B

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	59	0.27	0.73	16	K

Interfaces

1 interface between chains.

A–B · 572 Å² buried · 51 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

2DPB · Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine · 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 2DPB · PDBe 2DPB

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