scPDB - 3e9h entry

Protein Data Bank Entry:

PDB ID : 3e9h

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2008-08-22

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_GEOSE
AC:	Q9RHV9
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	6.1.1.6

Chains:

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

Ligand binding site composition:

B-Factor:	19.408
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.169	921.375

% Hydrophobic	% Polar
30.77	69.23
According to VolSite

Ligand :

HET Code:	KAA
Formula:	C16H27N8O7S
Molecular weight:	475.500 g/mol
DrugBank ID:	-
Buried Surface Area:	81.66 %
Polar Surface area:	257.5 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
37.0329	-124.07	27.6052

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
N	O	GLY- 207	2.93	162.11	H-Bond (Ligand Donor)	false
NZ	OE1	GLU- 231	2.89	0	Ionic (Ligand Cationic)	false
NZ	OE2	GLU- 231	2.89	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 231	2.62	0	Ionic (Ligand Cationic)	false
NZ	OE2	GLU- 231	2.89	128.03	H-Bond (Ligand Donor)	false
N	OE1	GLU- 231	2.62	133.93	H-Bond (Ligand Donor)	false
O1S	NH1	ARG- 253	3.02	141.35	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 253	2.89	148.93	H-Bond (Protein Donor)	false
N6	OE1	GLU- 255	3.11	125.88	H-Bond (Ligand Donor)	false
N1	N	ASN- 262	3.23	160.61	H-Bond (Protein Donor)	false
N6	O	ASN- 262	3.12	137.89	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 265	3.86	0	Hydrophobic	false
DuAr	DuAr	PHE- 265	3.45	0	Aromatic Face/Face	false
C5'	CE	MET- 267	3.54	0	Hydrophobic	false
CB	CG	GLU- 269	4.31	0	Hydrophobic	false
N	OE1	GLU- 269	2.89	150.15	H-Bond (Ligand Donor)	false
N	OE1	GLU- 269	2.89	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 269	3.52	0	Ionic (Ligand Cationic)	false
NZ	OH	TYR- 271	2.91	161.7	H-Bond (Ligand Donor)	false
CG	CZ	TYR- 271	4.45	0	Hydrophobic	false
O2'	O	GLU- 411	3.32	167.27	H-Bond (Ligand Donor)	false
N8	OD1	ASN- 414	3.06	159.11	H-Bond (Ligand Donor)	false
CD	CZ	PHE- 416	3.46	0	Hydrophobic	false
NZ	OE2	GLU- 418	3.36	143.03	H-Bond (Ligand Donor)	false
NZ	OE1	GLU- 418	2.69	154.45	H-Bond (Ligand Donor)	false
NZ	OE2	GLU- 418	3.36	0	Ionic (Ligand Cationic)	false
NZ	OE1	GLU- 418	2.69	0	Ionic (Ligand Cationic)	false
C2'	CD	ARG- 470	3.98	0	Hydrophobic	false
N3	O	HOH- 779	2.93	179.95	H-Bond (Protein Donor)	false
N7	O	HOH- 780	3.02	156.33	H-Bond (Protein Donor)	false