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A trigonal form of the idarubicin-D(CGATCG) complex: crystal and molecular structure at 2.0 ångströms resolution

Analyse A trigonal form of the idarubicin-D(CGATCG) complex: crystal and molecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 198D
Type: DNA
Length: 24 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
Ligands: DM5, SPM

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(CPGPAPTPCPG)-3')	dna	6	—	—

Ligands and binding sites

DM5 · Idarubicin · ligand · 4 copies · chains A, B, C, D
SPM · Spermine · ligand · chains A

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

Interfaces

6 interfaces between chains.

C–D · 286 Å² buried · 25 hydrogen bonds · nucleic-nucleic
A–B · 284 Å² buried · 22 hydrogen bonds · nucleic-nucleic
B–D · 91 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–C · 91 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 47 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

198D · A trigonal form of the idarubicin-D(CGATCG) complex: crystal and molecular structure at… · the same entry in another collection · chain C against C, 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 198D · PDBe 198D

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