scPDB - 1jil entry

Protein Data Bank Entry:

PDB ID : 1jil

Resolution :2.200 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:	34.825
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.525	843.750

% Hydrophobic	% Polar
30.80	69.20
According to VolSite

Ligand :

HET Code:	485
Formula:	C17H24N2O8
Molecular weight:	384.381 g/mol
DrugBank ID:	-
Buried Surface Area:	71.69 %
Polar Surface area:	187.02 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
31.9336	11.0808	83.1016

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
O1	OH	TYR- 36	2.84	166.04	H-Bond (Protein Donor)	false
C27	SG	CYS- 37	4.03	0	Hydrophobic	false
O16	N	ASP- 40	2.74	163.22	H-Bond (Protein Donor)	false
O17	NE2	HIS- 50	2.68	149.19	H-Bond (Protein Donor)	false
C27	CB	HIS- 50	4.37	0	Hydrophobic	false
C27	CG	PRO- 53	4.08	0	Hydrophobic	false
C21	CG	PRO- 53	3.91	0	Hydrophobic	false
C27	CE1	PHE- 54	3.63	0	Hydrophobic	false
C7	CD2	LEU- 70	3.67	0	Hydrophobic	false
C6	CB	THR- 75	4.48	0	Hydrophobic	false
C7	CG2	THR- 75	4.31	0	Hydrophobic	false
N10	OD2	ASP- 80	2.79	161.09	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 80	2.79	0	Ionic (Ligand Cationic)	false
N10	OH	TYR- 170	2.94	155.03	H-Bond (Ligand Donor)	false
N10	OE1	GLN- 174	2.72	145.62	H-Bond (Ligand Donor)	false
C2	CG	GLN- 174	3.53	0	Hydrophobic	false
O1	OD2	ASP- 177	2.57	165.04	H-Bond (Ligand Donor)	false
C2	CB	ASP- 177	4.32	0	Hydrophobic	false
O26	N	GLY- 193	2.92	163.49	H-Bond (Protein Donor)	false
O24	OD1	ASP- 195	2.68	164.63	H-Bond (Ligand Donor)	false
C19	CG	GLN- 196	4.16	0	Hydrophobic	false