scPDB - 4jyz entry

Protein Data Bank Entry:

PDB ID : 4jyz

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2013-04-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamine--tRNA ligase
ID:	SYQ_ECOLI
AC:	P00962
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.18

Chains:

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

Ligand binding site composition:

B-Factor:	39.468
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.236	681.750

% Hydrophobic	% Polar
43.07	56.93
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	65.4 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
20.093	42.2578	-11.3052

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
C4'	CE1	PHE- 31	3.76	0	Hydrophobic	false
O2A	N	GLU- 34	3.43	148.22	H-Bond (Protein Donor)	false
O2G	NE2	HIS- 40	2.92	173.66	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 43	3.34	133.94	H-Bond (Protein Donor)	false
C4'	CB	SER- 46	4.44	0	Hydrophobic	false
C1'	CB	SER- 46	3.99	0	Hydrophobic	false
O4'	OG	SER- 46	3.2	141	H-Bond (Protein Donor)	false
O2'	OG1	THR- 230	3.15	173.61	H-Bond (Protein Donor)	false
C1'	CG2	THR- 230	4.26	0	Hydrophobic	false
O1G	NH2	ARG- 260	3.19	125.64	H-Bond (Protein Donor)	false
N6	O	LEU- 261	3.33	161.96	H-Bond (Ligand Donor)	false
N1	N	LEU- 261	2.98	172.32	H-Bond (Protein Donor)	false
O2G	N	LYS- 270	3.5	130.21	H-Bond (Protein Donor)	false
O3G	N	LYS- 270	3.11	155.07	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 270	2.78	134.99	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 270	2.74	135.46	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 270	2.78	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 270	2.74	0	Ionic (Protein Cationic)	false