scPDB - 2z3n entry

Protein Data Bank Entry:

PDB ID : 2z3n

Resolution :2.500 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
A	100 %

Ligand binding site composition:

B-Factor:	56.290
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.652	739.125

% Hydrophobic	% Polar
37.44	62.56
According to VolSite

Ligand :

HET Code:	PHE_ARG_TYR_LEU_GLY
Formula:	C32H47N8O7
Molecular weight:	655.765 g/mol
DrugBank ID:	-
Buried Surface Area:	60.15 %
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
23.1985	6.91368	12.4227

Binding mode :

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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
CD	CE1	PHE- 47	3.38	0	Hydrophobic	false
NE	O	PRO- 48	3.3	137.78	H-Bond (Ligand Donor)	false
CD	CD2	TRP- 49	3.67	0	Hydrophobic	false
CG	CE2	TRP- 49	4.04	0	Hydrophobic	false
CE1	CB	TRP- 111	3.49	0	Hydrophobic	false
CB	CD1	ILE- 112	4.26	0	Hydrophobic	false
CG	CG1	ILE- 112	4.03	0	Hydrophobic	false
CE2	SD	MET- 144	4.06	0	Hydrophobic	false
CZ	CE	MET- 144	3.77	0	Hydrophobic	false
CZ	OE2	GLU- 156	3.52	0	Ionic (Ligand Cationic)	false
CZ	OE1	GLU- 156	3.41	0	Ionic (Ligand Cationic)	false
NH1	OE2	GLU- 156	3.06	149.23	H-Bond (Ligand Donor)	false
NH2	OE2	GLU- 156	3.08	147.43	H-Bond (Ligand Donor)	false
N	O	GLU- 156	3.49	159.3	H-Bond (Ligand Donor)	false
CB	CB	SER- 157	3.69	0	Hydrophobic	false
CE1	SD	MET- 158	4.24	0	Hydrophobic	false
CD1	CE	MET- 158	3.48	0	Hydrophobic	false
CE2	CG	MET- 158	3.66	0	Hydrophobic	false
N	O	CYS- 187	3.02	170.6	H-Bond (Ligand Donor)	false
CD1	SG	CYS- 187	4.4	0	Hydrophobic	false
N	OE1	GLN- 188	2.73	163.04	H-Bond (Ligand Donor)	false
NH2	OE1	GLN- 188	2.74	128.58	H-Bond (Ligand Donor)	false
CB	CB	GLN- 188	4.05	0	Hydrophobic	false