MolNFT v1 · #65115 · DNA

Calcium bound to the holliday junction sequence D(TCGGCGCCGA)4

3GNK · 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3': “Calcium bound to the holliday junction sequence D(TCGGCGCCGA)4”. X-ray diffraction, 2 ligands (CA, NA), 2 pockets (best druggability 0.46). MolNFT v1 #65115 on GenesisL1: 3D structure…

PDB: 3GNK
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
Ligands: CA, NA
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, D, C
NA · Sodium ion · metal · 2 copies · chains A, B, D

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

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	229	0.46	0.74	18	NA
2	173	0.42	0.74	15	empty

Interfaces

6 interfaces between chains.

C–D · 324 Å² buried · 28 hydrogen bonds · nucleic-nucleic
A–B · 318 Å² buried · 29 hydrogen bonds · nucleic-nucleic
B–D · 226 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–D · 225 Å² buried · 23 hydrogen bonds · nucleic-nucleic
B–C · 212 Å² buried · 21 hydrogen bonds · nucleic-nucleic

Compared structures

3GNK · Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4 · 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 3GNK · PDBe 3GNK

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.