MolNFT v1 · #74092 · DNA

Structural basis for cyclic py-im polyamide allosteric inhibition of nuclear receptor binding

3OMJ · 5'-D(*CP*(C38)P*AP*GP*TP*AP*CP*TP*GP*G)-3': “Structural basis for cyclic py-im polyamide allosteric inhibition of nuclear receptor binding”. X-ray diffraction, 2 ligands (1P2, CA). MolNFT v1 #74092 on GenesisL1: 3D structure…

PDB: 3OMJ
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*(C38)P*AP*GP*TP*AP*CP*TP*GP*G)-3'
Ligands: 1P2, CA

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-D(CP(C38)PAPGPTPAPCPTPGPG)-3'	dna	10	—	—

Ligands and binding sites

1P2 · (23R,52R)-23,52-diamino-5,11,17,28,34,40,46,57-octamethyl-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46,49,54,57,60,64-icosaazanonacyclo[54.2.1.1~4,7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45,48~]hexahexaconta-1(58),4(66),6,10(65),12,16(64),18,27(63),29,33(62),35,39(61),41,45(60),47,56(59)-hexadecaene-3,9,15,21,26,32,38,44,50,55-decone · ligand · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B

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

Interfaces

1 interface between chains.

A–B · 449 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

3OMJ · Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor… · 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 3OMJ · PDBe 3OMJ

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