scPDB - 2z3l entry

Protein Data Bank Entry:

PDB ID : 2z3l

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2007-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Leucyl/phenylalanyl-tRNA--protein transferase
ID:	LFTR_ECOLI
AC:	P0A8P1
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.3.2.6

Chains:

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

Ligand binding site composition:

B-Factor:	60.093
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.180	830.250

% Hydrophobic	% Polar
43.09	56.91
According to VolSite

Ligand :

HET Code:	PHE_ARG_TYR_LEU_GLY
Formula:	C32H47N8O7
Molecular weight:	655.765 g/mol
DrugBank ID:	-
Buried Surface Area:	56.98 %
Polar Surface area:	270.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	9
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-43.3325	-45.389	21.7369

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
NH2	OH	TYR- 42	3.07	124.14	H-Bond (Ligand Donor)	false
CD	CE1	PHE- 47	3.56	0	Hydrophobic	false
CB	CZ2	TRP- 49	3.95	0	Hydrophobic	false
CG	CE2	TRP- 49	3.47	0	Hydrophobic	false
CD	CD2	TRP- 49	3.62	0	Hydrophobic	false
CE2	CB	TRP- 111	3.95	0	Hydrophobic	false
CB	CD1	ILE- 112	4.26	0	Hydrophobic	false
CD2	CG1	ILE- 112	3.52	0	Hydrophobic	false
CE2	CE	MET- 144	3.65	0	Hydrophobic	false
CZ	OE2	GLU- 156	3.77	0	Ionic (Ligand Cationic)	false
CZ	OE1	GLU- 156	3.55	0	Ionic (Ligand Cationic)	false
NH2	OE1	GLU- 156	2.64	126.43	H-Bond (Ligand Donor)	false
CB	CB	SER- 157	3.4	0	Hydrophobic	false
CD1	CG	MET- 158	4.02	0	Hydrophobic	false
CD2	CG	MET- 158	4.38	0	Hydrophobic	false
CE1	CE	MET- 158	3.52	0	Hydrophobic	false
CZ	CD1	LEU- 170	4.39	0	Hydrophobic	false
CE1	CG2	ILE- 185	4.16	0	Hydrophobic	false
N	O	CYS- 187	3.01	150.56	H-Bond (Ligand Donor)	false
CD1	SG	CYS- 187	4.02	0	Hydrophobic	false
N	OE1	GLN- 188	3.1	167.82	H-Bond (Ligand Donor)	false
NE	OE1	GLN- 188	3.01	159.63	H-Bond (Ligand Donor)	false
CB	CB	GLN- 188	4.22	0	Hydrophobic	false
CD	CG	GLN- 188	4.49	0	Hydrophobic	false
CD1	CB	HIS- 193	4.5	0	Hydrophobic	false