MolNFT v1 · #21810 · DNA

Crystal structure of a DNA decamer containing a thymine- dimer

1SM5 · 5'-D(*GP*CP*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3': “Crystal structure of a DNA decamer containing a thymine- dimer”. X-ray diffraction, 1 pocket (best druggability 0.56). MolNFT v1 #21810 on GenesisL1: 3D structure, binding sites and…

PDB: 1SM5
Type: DNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*GP*CP*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3'; 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	5'-D(GPCP(BRU)PTPAPAPTP(BRU)PCPG)-3'	dna	10	—	—
B, D	5'-D(CPGPAPAPTPTPAPAPGPC)-3'	dna	10	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.56	0.74	21	empty

Interfaces

6 interfaces between chains.

A–B · 439 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–D · 438 Å² buried · 42 hydrogen bonds · nucleic-nucleic
B–D · 31 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–D · 19 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–C · 16 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1SM5 · Crystal Structure of a DNA Decamer Containing a Thymine-dimer · 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 1SM5 · PDBe 1SM5

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