scPDB - 3ts1 entry

Protein Data Bank Entry:

PDB ID : 3ts1

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1989-06-29

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_GEOSE
AC:	P00952
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	6.1.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	9.131
Number of residues:	48
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.014	877.500

% Hydrophobic	% Polar
39.23	60.77
According to VolSite

Ligand :

HET Code:	TYA
Formula:	C19H25N6O8P
Molecular weight:	496.411 g/mol
DrugBank ID:	-
Buried Surface Area:	70.83 %
Polar Surface area:	235.57 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-15.4322	15.3402	-6.21676

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
OH	OH	TYR- 34	3.27	146.18	H-Bond (Protein Donor)	false
C5'	CD1	PHE- 37	4.14	0	Hydrophobic	false
C4'	CE1	PHE- 37	4.2	0	Hydrophobic	false
O1P	N	ASP- 38	3.49	147.09	H-Bond (Protein Donor)	false
NH2	OD1	ASP- 38	3.73	0	Ionic (Ligand Cationic)	false
CB	CB	ASP- 38	4.33	0	Hydrophobic	false
C1'	CG2	THR- 51	4.29	0	Hydrophobic	false
CE2	CD2	LEU- 68	3.67	0	Hydrophobic	false
CZ	CD2	LEU- 68	3.56	0	Hydrophobic	false
CD2	CB	THR- 73	4.26	0	Hydrophobic	false
CE2	CG2	THR- 73	4.07	0	Hydrophobic	false
NH2	OD1	ASP- 78	2.71	0	Ionic (Ligand Cationic)	false
NH2	OH	TYR- 169	2.68	144.11	H-Bond (Ligand Donor)	false
NH2	OE1	GLN- 173	3.11	144.65	H-Bond (Ligand Donor)	false
CE1	CG	GLN- 173	3.92	0	Hydrophobic	false
CZ	CB	ASP- 176	4.42	0	Hydrophobic	false
OH	OD1	ASP- 176	2.65	174.07	H-Bond (Ligand Donor)	false
O3'	N	GLY- 192	3.42	173.76	H-Bond (Protein Donor)	false
O2'	N	GLY- 192	3.19	124.34	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 194	3.05	150.69	H-Bond (Ligand Donor)	false
C	CG	GLN- 195	4.34	0	Hydrophobic	false
C3'	CG	GLN- 195	4.23	0	Hydrophobic	false
O3'	O	HOH- 423	2.77	160.23	H-Bond (Ligand Donor)	false