MolNFT v1 · #67315 · DNA

A rare nucleotide base tautomer in the structure of an asymmetric DNA junction

3IGT · 5'-D(*CP*CP*GP*AP*GP*TP*CP*CP*TP*A)-3': “A rare nucleotide base tautomer in the structure of an asymmetric DNA junction”. X-ray diffraction, 2 pockets (best druggability 0.45). MolNFT v1 #67315 on GenesisL1: 3D structure, binding…

PDB: 3IGT
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*GP*AP*GP*TP*CP*CP*TP*A)-3'; 5'-D(*CP*TP*CP*AP*AP*CP*TP*CP*GP*G)-3'…
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(CPCPGPAPGPTPCPCPTPA)-3'	dna	10	—	—
B	5'-D(CPTPCPAPAPCPTPCPGPG)-3'	dna	10	—	—
C	5'-D(TPCPGPGPCPCPTPGPAPG)-3'	dna	10	—	—
D	5'-D(TPAPGPGPGPGPCPCPGPA)-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	231	0.45	0.73	22	empty
2	224	0.44	0.73	21	empty

Interfaces

6 interfaces between chains.

C–D · 296 Å² buried · 29 hydrogen bonds · nucleic-nucleic
A–B · 293 Å² buried · 28 hydrogen bonds · nucleic-nucleic
A–C · 230 Å² buried · 9 hydrogen bonds · nucleic-nucleic
B–C · 212 Å² buried · 16 hydrogen bonds · nucleic-nucleic
A–D · 205 Å² buried · 15 hydrogen bonds · nucleic-nucleic

Compared structures

3IGT · A rare nucleotide base tautomer in the structure of an asymmetric DNA junction · 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 3IGT · PDBe 3IGT

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