scPDB - 2zue entry

Protein Data Bank Entry:

PDB ID : 2zue

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Arginine--tRNA ligase
ID:	SYR_PYRHO
AC:	O59147
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	6.1.1.19

Chains:

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

Ligand binding site composition:

B-Factor:	25.207
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.845	1360.125

% Hydrophobic	% Polar
34.00	66.00
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	64.48 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
38.3982	-2.85726	29.9491

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
O1A	N	ASN- 129	2.87	178.34	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 132	2.91	155.96	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 132	2.67	155.6	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 132	2.91	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 132	2.81	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 132	2.67	0	Ionic (Protein Cationic)	false
O3G	NE2	HIS- 135	3.03	155.94	H-Bond (Protein Donor)	false
O1G	NE2	HIS- 138	3.18	129	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 138	3.43	156.6	H-Bond (Protein Donor)	false
O3'	N	GLY- 384	3.33	160.44	H-Bond (Protein Donor)	false
O2'	N	GLY- 384	2.71	124.68	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 386	2.77	155.82	H-Bond (Ligand Donor)	false
N3	OH	TYR- 415	3.14	159.28	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 417	3.6	0	Aromatic Face/Face	false
N6	O	VAL- 418	3.47	167.16	H-Bond (Ligand Donor)	false
N1	N	VAL- 418	3.19	165.86	H-Bond (Protein Donor)	false
O2B	MG	MG- 800	2.45	0	Metal Acceptor	false
N6	O	HOH- 1073	3.07	120.05	H-Bond (Ligand Donor)	false