scPDB - 1jik entry

Protein Data Bank Entry:

PDB ID : 1jik

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2001-07-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine--tRNA ligase
ID:	SYY_STAAE
AC:	A6QHR2
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	426430
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.202
Number of residues:	45
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.519	769.500

% Hydrophobic	% Polar
30.26	69.74
According to VolSite

Ligand :

HET Code:	545
Formula:	C21H33N3O9
Molecular weight:	471.501 g/mol
DrugBank ID:	-
Buried Surface Area:	72.89 %
Polar Surface area:	210.48 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	7
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
33.1944	11.1617	83.7076

Binding mode :

What is Poseview ?

2D View
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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
O13	OH	TYR- 36	3.34	164.16	H-Bond (Protein Donor)	false
C4	SG	CYS- 37	4.24	0	Hydrophobic	false
O28	O	GLY- 38	2.72	142.53	H-Bond (Ligand Donor)	false
C24	CB	ALA- 39	4.18	0	Hydrophobic	false
C14	CB	ASP- 40	4.48	0	Hydrophobic	false
C24	CB	ASP- 40	4	0	Hydrophobic	false
O23	N	ASP- 40	3.06	151.91	H-Bond (Protein Donor)	false
C27	CD2	LEU- 46	3.75	0	Hydrophobic	false
O29	O	GLY- 49	3.37	138.72	H-Bond (Ligand Donor)	false
C30	CB	HIS- 50	3.86	0	Hydrophobic	false
C30	CG	PRO- 53	3.39	0	Hydrophobic	false
C30	CE2	PHE- 54	3.97	0	Hydrophobic	false
C7	CD2	LEU- 70	3.41	0	Hydrophobic	false
C7	CG2	THR- 75	4.34	0	Hydrophobic	false
N16	OD2	ASP- 80	2.81	154.79	H-Bond (Ligand Donor)	false
N16	OD2	ASP- 80	2.81	0	Ionic (Ligand Cationic)	false
C27	CD1	ILE- 103	3.49	0	Hydrophobic	false
N16	OH	TYR- 170	2.73	148.43	H-Bond (Ligand Donor)	false
N16	OE1	GLN- 174	3.28	171.89	H-Bond (Ligand Donor)	false
C11	CG	GLN- 174	3.2	0	Hydrophobic	false
C12	CB	ASP- 177	4.26	0	Hydrophobic	false
C4	CG	GLN- 196	4.41	0	Hydrophobic	false