scPDB - 1tkg entry

Protein Data Bank Entry:

PDB ID : 1tkg

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2004-06-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Threonine--tRNA ligase
ID:	SYT_ECOLI
AC:	P0A8M3
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	11.243
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.023	442.125

% Hydrophobic	% Polar
53.44	46.56
According to VolSite

Ligand :

HET Code:	SSA
Formula:	C13H19N7O8S
Molecular weight:	433.397 g/mol
DrugBank ID:	DB03869
Buried Surface Area:	60.29 %
Polar Surface area:	250.09 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-7.74369	0.560241	19.6264

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
N8	NE2	HIS- 73	3.06	137.56	H-Bond (Ligand Donor)	false
CB	CB	ALA- 76	4.48	0	Hydrophobic	false
N10	NE2	HIS- 77	2.79	167.86	H-Bond (Ligand Donor)	false
OG	O	GLY- 95	2.54	176.54	H-Bond (Ligand Donor)	false
O9	N	GLY- 95	2.9	174.24	H-Bond (Protein Donor)	false
CB	CE2	TYR- 104	3.52	0	Hydrophobic	false
C2'	CG2	ILE- 159	3.86	0	Hydrophobic	false
C2'	CD1	ILE- 164	3.99	0	Hydrophobic	false
N6	O	LYS- 169	3.3	158.77	H-Bond (Ligand Donor)	false
N1	N	GLY- 171	3.03	162.27	H-Bond (Protein Donor)	false
N10	OD1	ASP- 180	3.51	0	Ionic (Ligand Cationic)	false
N10	O	MET- 181	2.88	173.03	H-Bond (Ligand Donor)	false
C5'	SG	CYS- 182	4.3	0	Hydrophobic	false
C1'	CG	ARG- 183	4.4	0	Hydrophobic	false
O3'	O	HOH- 508	2.93	179.98	H-Bond (Protein Donor)	false