MolNFT v1 · #153932 · DNA

Crystal structure of 5-hydoxylmethylcytosine containing decamer dsdna

6JV3 · DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3'): “Crystal structure of 5-hydoxylmethylcytosine containing decamer dsdna”. X-ray diffraction, 1 pocket (best druggability 0.36). MolNFT v1 #153932 on GenesisL1: 3D structure, binding…

PDB: 6JV3
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain.

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.36	0.72	16	empty

Interfaces

6 interfaces between chains.

C–D · 316 Å² buried · 39 hydrogen bonds · nucleic-nucleic
A–B · 299 Å² buried · 32 hydrogen bonds · nucleic-nucleic
A–D · 246 Å² buried · 7 hydrogen bonds · nucleic-nucleic
B–D · 216 Å² buried · 21 hydrogen bonds · nucleic-nucleic
A–C · 202 Å² buried · 15 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

6JV3 · Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA · 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 6JV3 · PDBe 6JV3

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