scPDB - 3bju entry

Protein Data Bank Entry:

PDB ID : 3bju

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2007-12-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lysine--tRNA ligase
ID:	SYK_HUMAN
AC:	Q15046
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.1.1.6

Chains:

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

Ligand binding site composition:

B-Factor:	20.979
Number of residues:	44
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	CA CA CA

Cavity properties

Ligandability	Volume (Å3)
0.813	1488.375

% Hydrophobic	% Polar
31.75	68.25
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	72.69 %
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
56.8326	23.0519	51.4737

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
O2B	NH1	ARG- 323	3.42	128.57	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 323	3.24	134.67	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 323	2.78	162.26	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 323	3.44	0	Ionic (Protein Cationic)	false
N6	OE1	GLU- 325	3.12	146.08	H-Bond (Ligand Donor)	false
O1G	NE2	HIS- 331	2.71	177.93	H-Bond (Protein Donor)	false
N6	O	ASN- 332	2.94	122.26	H-Bond (Ligand Donor)	false
N1	N	ASN- 332	3.21	165.18	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 335	3.83	0	Hydrophobic	false
DuAr	DuAr	PHE- 335	3.54	0	Aromatic Face/Face	false
C3'	CG	GLU- 494	4.5	0	Hydrophobic	false
O3'	OE2	GLU- 494	2.74	173.27	H-Bond (Ligand Donor)	false
O2'	O	ILE- 495	3.22	132.37	H-Bond (Ligand Donor)	false
O1A	ND2	ASN- 497	3.41	123.53	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 553	2.89	137.46	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 553	2.72	145.73	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 553	3.22	0	Ionic (Protein Cationic)	false
C2'	CG	ARG- 553	4.22	0	Hydrophobic	false
O1B	CA	CA- 606	2.26	0	Metal Acceptor	false
O1A	CA	CA- 606	2.28	0	Metal Acceptor	false
O1G	CA	CA- 607	2.14	0	Metal Acceptor	false
O2B	CA	CA- 607	2.24	0	Metal Acceptor	false
O3G	CA	CA- 608	2.27	0	Metal Acceptor	false
O1B	CA	CA- 608	2.69	0	Metal Acceptor	false
N3	O	HOH- 609	2.8	168.83	H-Bond (Protein Donor)	false
N7	O	HOH- 856	2.73	169.72	H-Bond (Protein Donor)	false