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Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP and met repressor-operator complexes

Analyse Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 250D
Type: DNA
Length: 48 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*GP*CP*TP*AP*GP*CP*G)-3')
Pockets: 3 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA (5'-D(CPGPCPTPAPGPCPG)-3')	dna	8	—	—

Pockets

3 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	95	0.36	0.76	10	empty
2	58	0.26	0.73	10	empty
3	52	0.26	0.74	11	empty

Interfaces

11 interfaces between chains.

A–B · 401 Å² buried · 39 hydrogen bonds · nucleic-nucleic
E–F · 397 Å² buried · 38 hydrogen bonds · nucleic-nucleic
C–D · 395 Å² buried · 38 hydrogen bonds · nucleic-nucleic
B–C · 190 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–D · 182 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Compared structures

250D · Structural comparison between the D(CTAG) sequence in oligonucleotides and TRP and met… · 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 250D · PDBe 250D

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