MolNFT v1 · #93975 · protein + DNA

Structure of actinomycin D D(ATGCGGCAT) complex

4HIV · DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3'): “Structure of actinomycin D D(ATGCGGCAT) complex”. X-ray diffraction, 1 ligand (PXZ). MolNFT v1 #93975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HIV
Type: protein + DNA
Length: 38 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*AP*T)-3'); Actinomycin D
Ligands: PXZ

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(APTPGPCPGPGPCPAP*T)-3')	dna	9	—	—
C, D	Actinomycin D	protein	10	0% helix, 0% strand	—

Ligands and binding sites

PXZ · 2-amino-1,9-dicarbonyl-4,6-dimethyl-10-dehydro-phenoxazin-3-one · ligand · 2 copies · chains A, B, C, D

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

Interfaces

6 interfaces between chains.

A–B · 363 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–D · 270 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 234 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 177 Å² buried · 1 hydrogen bond · protein-nucleic
A–C · 176 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 8 modified, 4 covalent, 4 d-amino (methylation, covalent ligand, D-amino acid).

Compared structures

4HIV · Structure of actinomycin D d(ATGCGGCAT) complex · 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 4HIV · PDBe 4HIV

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