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(-)-duocarmycin sa covalently linked to duplex DNA

Analyse (-)-duocarmycin sa covalently linked to duplex DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DSM
Type: DNA
Length: 22 nucleotides
Chains: 2
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3'; 5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3'
Ligands: DSA
Pockets: 1 · best druggability 0.25

Structure

solution nmr · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(GPAPCPTPAPAPTPTPGPAP*C)-3'	dna	11	—	—
B	5'-D(GPTPCPAPAPTPTPAPGPTP*C)-3'	dna	11	—	—

Ligands and binding sites

DSA · 4-hydroxy-8-methyl-6-(4,5,6-trimethoxy-1H-indole-2-carbonyl)-3,6,7,8-tetrahydro-3,6-diaza-as-indacene-2-carboxylic acid methyl ester · ligand · 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	51	0.25	0.73	10	DSA

Interfaces

1 interface between chains.

A–B · 476 Å² buried · 51 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1DSM · (-)-duocarmycin SA covalently linked to duplex DNA · 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 1DSM · PDBe 1DSM

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