scPDB - 1p0e entry

Protein Data Bank Entry:

PDB ID : 1p0e

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2003-04-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Queuine tRNA-ribosyltransferase
ID:	TGT_ZYMMO
AC:	P28720
Organism:	Zymomonas mobilis subsp. mobilis
Reign:	Bacteria
TaxID:	264203
EC Number:	2.4.2.29

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	44.494
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.356	658.125

% Hydrophobic	% Polar
41.54	58.46
According to VolSite

Ligand :

HET Code:	PRF
Formula:	C7H10N5O
Molecular weight:	180.187 g/mol
DrugBank ID:	DB03304
Buried Surface Area:	78.7 %
Polar Surface area:	110.91 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
25.8568	29.1317	21.6605

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
N3	OD2	ASP- 102	3.46	134.69	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 102	2.99	166.2	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 102	2.95	155.99	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 106	3.72	0	Aromatic Face/Face	false
N2	OD1	ASP- 156	2.76	169.26	H-Bond (Ligand Donor)	false
O6	NE2	GLN- 203	3.25	173.54	H-Bond (Protein Donor)	false
O6	N	GLY- 230	2.85	173.51	H-Bond (Protein Donor)	false
N11	O	LEU- 231	2.68	165.35	H-Bond (Ligand Donor)	false