MolNFT v1 · #98033 · DNA

Linear structure of the holliday junction sequence (tcggcgccga)

4KWX · 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3': “Linear structure of the holliday junction sequence (tcggcgccga)”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.57). MolNFT v1 #98033 on GenesisL1: 3D structure, binding…

PDB: 4KWX
Type: DNA
Length: 60 nucleotides
Chains: 6
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: MG
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains A, B, C, E, D, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	273	0.57	0.78	28	MG
2	222	0.48	0.75	23	MG
3	234	0.47	0.74	17	empty
4	57	0.32	0.77	12	MG

Interfaces

12 interfaces between chains.

E–F · 484 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–D · 483 Å² buried · 44 hydrogen bonds · nucleic-nucleic
A–B · 482 Å² buried · 43 hydrogen bonds · nucleic-nucleic
A–C · 126 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–D · 95 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

4KWX · Linear structure of the Holliday junction sequence (TCGGCGCCGA) · 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 4KWX · PDBe 4KWX

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