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CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate lesion

Analyse CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GJ2
Type: DNA
Length: 25 nucleotides
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*AP*AP*AP*G)-3'; 5'-D(P*AP*CP*TP*GP*GP*G)-3'…
Ligands: PGA, BLB, PEO, 3CO, O

Structure

solution nmr · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(CPCPAPAPAPG)-3'	dna	6	—	—
B	5'-D(PAPCPTPGPGPG)-3'	dna	6	—	—
C	5'-D(CPCPCPAPGPTPAPCPTPTPTPGP*G)-3'	dna	13	—	—

Ligands and binding sites

PGA · 2-phosphoglycolic acid · ligand · chains A
BLB · Bleomycin B2 · ligand · chains A, B, C
PEO · Hydrogen peroxide · ligand · chains C
3CO · Cobalt (III) ion · metal
O · Oxygen atom · ion · chains B

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

Interfaces

2 interfaces between chains.

A–C · 321 Å² buried · 29 hydrogen bonds · nucleic-nucleic
B–C · 292 Å² buried · 31 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1GJ2 · CO(III)-bleomycin-ooh bound to an oligonucleotide containing a phosphoglycolate lesion · the same entry in another collection · chain B against B, 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 1GJ2 · PDBe 1GJ2

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