MolNFT v1 · #126423 · DNA

Structure of DNA tetrameric agcga-quadruplex adopted by 15-mer D(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

5M2L · DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)- 3'): “Structure of DNA tetrameric agcga-quadruplex adopted by 15-mer D(GCGAGGGAGCGAGGG), VK34, oligonucleotide…”. Solution nmr, 4 pockets (best druggability 0.31). MolNFT v1…

PDB: 5M2L
Type: DNA
Length: 60 nucleotides
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)- 3')
Pockets: 4 · best druggability 0.31

Structure

solution nmr · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	DNA (5'-D(GPCPGPAPGPGPGPAPGPCPGPAPGPGP*G)- 3')	dna	15	—	—

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.31	0.75	8	empty
2	63	0.31	0.76	8	empty
3	70	0.30	0.75	11	empty
4	65	0.28	0.74	11	empty

Interfaces

6 interfaces between chains.

B–C · 819 Å² buried · 44 hydrogen bonds · nucleic-nucleic
A–D · 786 Å² buried · 39 hydrogen bonds · nucleic-nucleic
C–D · 745 Å² buried · 44 hydrogen bonds · nucleic-nucleic
A–B · 707 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–C · 334 Å² buried · 15 hydrogen bonds · nucleic-nucleic

Compared structures

5M2L · Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34… · 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 5M2L · PDBe 5M2L

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