MolNFT v2 · #110771 · protein + DNA

Structure of AgrA LytTR domain in complex with promoters

4XYQ · DNA (5'-D(*TP*TP*TP*AP*AP*CP*AP*GP*TP*TP*AP*AP*GP*TP*AP*T)-3…: “Structure of AgrA LytTR domain in complex with promoters”. X-ray diffraction at 2.4, 3 pockets (best druggability 0.45). MolNFT v2 #110771 on GenesisL1: 3D structure…

PDB: 4XYQ
Type: protein + DNA
Length: 135 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Staphylococcus aureus (strain COL); SYNTHETIC CONSTRUCT
Molecule: DNA (5'-D(*TP*TP*TP*AP*AP*CP*AP*GP*TP*TP*AP*AP*GP*TP*AP*T)-3'); DNA…
UniProt: Q5HEG2
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · resolution 2.4 · 3 distinct chains · 16% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (5'-D(TPTPTPAPAPCPAPGPTPTPAPAPGPTPAPT)-3')	dna	16	—	—
C	DNA (5'-D(APAPTPAPCPTPTPAPAPCPTPGPTPTPAPA)-3')	dna	16	—	—
A	Accessory gene regulator A	protein	103	16% helix, 49% strand	Q5HEG2

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains B, A

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

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	164	0.45	0.76	22	empty
2	110	0.38	0.76	16	empty
3	53	0.25	0.73	11	empty

Interfaces

3 interfaces between chains.

B–C · 666 Å² buried · 48 hydrogen bonds · nucleic-nucleic
C–A · 502 Å² buried · 8 hydrogen bonds · protein-nucleic
B–A · 360 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

4XYQ · Structure of agra lyttr domain in complex with promoters · the same entry in another collection · chain A against A, TM-score 1.00
Q5HEG2 · AlphaFold monomer V2.0 prediction for accessory gene regulator a (Q5HEG2) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q5HEG2
Elsewhere: RCSB PDB 4XYQ · PDBe 4XYQ · UniProt Q5HEG2

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