MolNFT v1 · #93102 · DNA

DNA holliday junction stabilized by fluorine halogen bond. F2J construct of related reference.

4GSI · DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3'): “DNA holliday junction stabilized by fluorine halogen bond. F2J construct of related reference.”. X-ray diffraction, 2 pockets (best druggability 0.49). MolNFT v1 #93102 on…

PDB: 4GSI
Type: DNA
Length: 80 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UFP)P*CP*GP*G)-3'); DNA…
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F, H	DNA (5'-D(CPCPGPGPTPAP(UFP)PCPGPG)-3')	dna	10	—	—
B, D, E, G	DNA (5'-D(CPCPGPAPTPAPCPCPGPG)-3')	dna	10	—	—

Pockets

2 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	245	0.49	0.75	42	empty
2	235	0.46	0.74	46	empty

Interfaces

28 interfaces between chains.

A–E · 1001 Å² buried · 414 hydrogen bonds · nucleic-nucleic
C–G · 930 Å² buried · 387 hydrogen bonds · nucleic-nucleic
B–F · 800 Å² buried · 348 hydrogen bonds · nucleic-nucleic
D–H · 777 Å² buried · 383 hydrogen bonds · nucleic-nucleic
C–H · 313 Å² buried · 27 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

4GSI · DNA Holliday junction stabilized by fluorine halogen bond. F2J construct of related… · 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 4GSI · PDBe 4GSI

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