Research workbench

Cryo EM structure of the conjugative relaxase trai of the F/R1 plasmid system

Analyse Cryo EM structure of the conjugative relaxase trai of the F/R1 plasmid system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N8O
Type: protein + DNA
Length: 1,450 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA helicase I; DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
UniProt: Q6TDU5
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 30% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA helicase I	protein	1432	30% helix, 13% strand	Q6TDU5
C	DNA (5'- D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	dna	18	—	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.87	0.89	121	empty
2	217	0.81	0.94	46	empty
3	573	0.81	0.87	69	empty
4	395	0.81	0.90	59	empty
5	300	0.71	0.85	41	empty

Interfaces

1 interface between chains.

A–C · 2626 Å² buried · 32 hydrogen bonds · protein-nucleic

Compared structures

5N8O · Cryo EM structure of the conjugative relaxase TraI of the F/R1 plasmid system · 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
Every structure of UniProt Q6TDU5
Elsewhere: RCSB PDB 5N8O · PDBe 5N8O · UniProt Q6TDU5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.