scPDB - 3jxe entry

Protein Data Bank Entry:

PDB ID : 3jxe

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2009-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan--tRNA ligase
ID:	SYW_PYRHO
AC:	O59584
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	70.391
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.141	735.750

% Hydrophobic	% Polar
30.28	69.72
According to VolSite

Ligand :

HET Code:	TYM
Formula:	C21H24N7O8P
Molecular weight:	533.431 g/mol
DrugBank ID:	DB01831
Buried Surface Area:	82.33 %
Polar Surface area:	248.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-38.8645	29.2362	10.9474

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
NE1	OH	TYR- 77	2.68	153.7	H-Bond (Ligand Donor)	false
CH2	CB	THR- 78	4.39	0	Hydrophobic	false
O1P	CZ	ARG- 80	3.81	0	Ionic (Protein Cationic)	false
O1P	NH1	ARG- 80	3.08	120.47	H-Bond (Protein Donor)	false
C5'	CD	ARG- 80	4.36	0	Hydrophobic	false
O1P	N	GLY- 81	2.8	163.02	H-Bond (Protein Donor)	false
C5'	CB	HIS- 90	4.39	0	Hydrophobic	false
C1'	CG	PRO- 93	3.82	0	Hydrophobic	false
C4'	CG	PRO- 93	4.02	0	Hydrophobic	false
CB	CG2	THR- 113	3.93	0	Hydrophobic	false
NH3	OE1	GLU- 116	2.69	148	H-Bond (Ligand Donor)	false
NH3	OE1	GLU- 116	2.69	0	Ionic (Ligand Cationic)	false
NH3	OE2	GLU- 116	3.18	0	Ionic (Ligand Cationic)	false
O	NZ	LYS- 117	3.23	134.1	H-Bond (Protein Donor)	false
NH3	OE1	GLN- 198	3.05	177.01	H-Bond (Ligand Donor)	false
CE2	CG	GLN- 198	4.21	0	Hydrophobic	false
CH2	CG2	ILE- 211	3.85	0	Hydrophobic	false
CZ3	CB	ALA- 213	3.73	0	Hydrophobic	false
O2'	N	ALA- 214	2.88	145.37	H-Bond (Protein Donor)	false
C1'	CB	ALA- 214	3.9	0	Hydrophobic	false
O2'	OD1	ASP- 216	2.86	160.2	H-Bond (Ligand Donor)	false
C2'	CG	GLN- 217	4.11	0	Hydrophobic	false
CZ3	CG	GLN- 217	3.85	0	Hydrophobic	false
N1	N	VAL- 244	2.85	176.71	H-Bond (Protein Donor)	false
N6	O	VAL- 244	3.49	175.77	H-Bond (Ligand Donor)	false
N7	NZ	LYS- 253	2.7	147.58	H-Bond (Protein Donor)	false
N6	O	MET- 254	3.42	132.11	H-Bond (Ligand Donor)	false