scPDB - 2j5b entry

Protein Data Bank Entry:

PDB ID : 2j5b

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-09-13

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_MIMIV
AC:	Q5UPJ7
Organism:	Acanthamoeba polyphaga mimivirus
Reign:	Viruses
TaxID:	212035
EC Number:	6.1.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	39.084
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.924	691.875

% Hydrophobic	% Polar
38.54	61.46
According to VolSite

Ligand :

HET Code:	TYE
Formula:	C9H14NO2
Molecular weight:	168.213 g/mol
DrugBank ID:	-
Buried Surface Area:	57.74 %
Polar Surface area:	68.1 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
29.6096	55.8919	18.7039

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	2.6	166.51	H-Bond (Protein Donor)	false
N	OE1	GLU- 38	3.75	0	Ionic (Ligand Cationic)	false
CB	CG	GLU- 38	4.17	0	Hydrophobic	false
CD1	CB	ALA- 70	4.03	0	Hydrophobic	false
N	OE1	GLN- 165	3.37	172.02	H-Bond (Ligand Donor)	false
CZ	CG	GLN- 165	3.58	0	Hydrophobic	false
OH	OD2	ASP- 168	2.53	148.54	H-Bond (Ligand Donor)	false
CE2	CD2	LEU- 182	3.82	0	Hydrophobic	false