scPDB - 1q65 entry

Protein Data Bank Entry:

PDB ID : 1q65

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-08-12

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:	30.950
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.278	388.125

% Hydrophobic	% Polar
46.96	53.04
According to VolSite

Ligand :

HET Code:	BHB
Formula:	C13H20N5OS
Molecular weight:	294.396 g/mol
DrugBank ID:	DB04004
Buried Surface Area:	55.52 %
Polar Surface area:	123.24 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
15.787	17.4447	19.8568

Binding mode :

What is Poseview ?

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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	OD1	ASP- 102	2.86	168.7	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 102	3.38	133.45	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 102	2.87	144.39	H-Bond (Ligand Donor)	false
C3	CB	TYR- 106	4.23	0	Hydrophobic	false
S1	CD2	TYR- 106	4.14	0	Hydrophobic	false
C16	CG	GLN- 107	3.53	0	Hydrophobic	false
N2	OD1	ASP- 156	2.92	154.62	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 156	3.48	133	H-Bond (Ligand Donor)	false
O1	NE2	GLN- 203	3.17	160.83	H-Bond (Protein Donor)	false
O1	N	GLY- 230	2.89	147.37	H-Bond (Protein Donor)	false
N4	O	LEU- 231	2.97	163.97	H-Bond (Ligand Donor)	false
C3	CE	MET- 260	3.88	0	Hydrophobic	false
C41	SD	MET- 260	3.98	0	Hydrophobic	false
C6	CB	MET- 260	4.03	0	Hydrophobic	false