MolNFT v1 · #57107 · protein + DNA

Selectivity of F8-actinomycin D for RNA:DNA hybrids and its anti- leukemia activity

316D · DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3'): “Selectivity of F8-actinomycin D for RNA:DNA hybrids and its anti- leukemia activity”. X-ray diffraction, 1 ligand (PXF). MolNFT v1 #57107 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 316D
Type: protein + DNA
Length: 26 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3'); 8-fluoro-actinomycin D
Ligands: PXF

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(GPAPAPGPCPTPTPC)-3')	dna	8	—	—
C	8-fluoro-actinomycin D	protein	10	0% helix, 20% strand	—

Ligands and binding sites

PXF · 2-amino-1,9-dicarbonyl-4,6-dimethyl-10-dehydro-8-fluoro-3-oxophenoxazine · ligand · chains A, B, C

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

Interfaces

3 interfaces between chains.

A–B · 367 Å² buried · 22 hydrogen bonds · nucleic-nucleic
B–C · 263 Å² buried · 5 hydrogen bonds · protein-nucleic
A–C · 243 Å² buried · 3 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified, 2 covalent, 2 d-amino (methylation, covalent ligand, D-amino acid).

Compared structures

316D · Selectivity of F8-actinomycin D for RNA:DNA hybrids and its anti-leukemia activity · 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 316D · PDBe 316D

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