scPDB - 3zgz entry

Protein Data Bank Entry:

PDB ID : 3zgz

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2012-12-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Leucine--tRNA ligase
ID:	SYL_ECOLI
AC:	P07813
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.024
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.752	1690.875

% Hydrophobic	% Polar
36.93	63.07
According to VolSite

Ligand :

HET Code:	84T
Formula:	C16H24N6O8P
Molecular weight:	459.371 g/mol
DrugBank ID:	-
Buried Surface Area:	80.16 %
Polar Surface area:	227.8 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-51.3323	31.675	-36.8522

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
CB	CB	MET- 40	4.4	0	Hydrophobic	false
CD1	CB	MET- 40	3.79	0	Hydrophobic	false
C2'	SD	MET- 40	4.09	0	Hydrophobic	false
C3'	CB	MET- 40	3.9	0	Hydrophobic	false
CD1	CD2	LEU- 41	3.95	0	Hydrophobic	false
O1P	N	TYR- 43	2.74	158.77	H-Bond (Protein Donor)	false
O1P	NE2	HIS- 52	2.81	171.12	H-Bond (Protein Donor)	false
C1'	CB	ASN- 55	4.1	0	Hydrophobic	false
OH	OD2	ASP- 80	2.68	155.13	H-Bond (Ligand Donor)	false
CD2	CE1	PHE- 493	4.32	0	Hydrophobic	false
CD2	CB	SER- 496	3.62	0	Hydrophobic	false
CD1	CE1	TYR- 499	4.4	0	Hydrophobic	false
O2'	OE2	GLU- 532	2.62	150.47	H-Bond (Ligand Donor)	false
O	NE2	HIS- 533	2.7	156.32	H-Bond (Protein Donor)	false
CD2	CB	HIS- 537	4.18	0	Hydrophobic	false
N1	N	VAL- 569	2.71	170.23	H-Bond (Protein Donor)	false
N6	O	VAL- 569	3.05	167.85	H-Bond (Ligand Donor)	false
N6	O	MET- 620	3.33	155.21	H-Bond (Ligand Donor)	false
O2P	NZ	LYS- 622	2.74	153.42	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 622	2.74	0	Ionic (Protein Cationic)	false