MolNFT v1 · #120267 · DNA

Crystal structure of D(GTGGAATGGAAC)

5GUN · DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3'): “Crystal structure of D(GTGGAATGGAAC)”. X-ray diffraction, 1 ligand (CO), 1 pocket (best druggability 0.58). MolNFT v1 #120267 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5GUN
Type: DNA
Length: 72 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
Ligands: CO
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	DNA (5'-D(GPTPGPGPAPAPTPGPGPAPAPC)-3')	dna	12	—	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 8 copies · chains A, B, E, F, C, D

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

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	342	0.58	0.77	41	CO

Interfaces

14 interfaces between chains.

A–B · 875 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–D · 860 Å² buried · 57 hydrogen bonds · nucleic-nucleic
E–F · 858 Å² buried · 49 hydrogen bonds · nucleic-nucleic
A–F · 131 Å² buried · 3 hydrogen bonds · nucleic-nucleic
D–E · 84 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Compared structures

5GUN · Crystal structure of d(GTGGAATGGAAC) · 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 5GUN · PDBe 5GUN

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