scPDB - 3e9i entry

Protein Data Bank Entry:

PDB ID : 3e9i

Resolution :2.200 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:	14.871
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.300	982.125

% Hydrophobic	% Polar
27.84	72.16
According to VolSite

Ligand :

HET Code:	XAH
Formula:	C16H28N8O8P
Molecular weight:	491.416 g/mol
DrugBank ID:	-
Buried Surface Area:	77.94 %
Polar Surface area:	272.08 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
116.194	-127.121	27.2845

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
N7	O	GLY- 207	3.13	130.1	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 231	2.88	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 231	3.44	0	Ionic (Ligand Cationic)	false
N7	OE2	GLU- 231	2.86	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 231	3.44	124.74	H-Bond (Ligand Donor)	false
N7	OE2	GLU- 231	2.86	172.99	H-Bond (Ligand Donor)	false
O11	NH1	ARG- 253	3.07	165.52	H-Bond (Protein Donor)	false
O13	NH2	ARG- 253	3.15	161.25	H-Bond (Protein Donor)	false
N33	OE1	GLU- 255	3.04	134.01	H-Bond (Ligand Donor)	false
N31	N	ASN- 262	3.13	161.91	H-Bond (Protein Donor)	false
N33	O	ASN- 262	3.22	128.44	H-Bond (Ligand Donor)	false
C23	CE2	PHE- 265	3.87	0	Hydrophobic	false
DuAr	DuAr	PHE- 265	3.59	0	Aromatic Face/Face	false
C5	SD	MET- 267	4.07	0	Hydrophobic	false
C16	SD	MET- 267	3.92	0	Hydrophobic	false
N7	OE2	GLU- 269	2.98	156.5	H-Bond (Ligand Donor)	false
N7	OE2	GLU- 269	2.98	0	Ionic (Ligand Cationic)	false
N7	OE1	GLU- 269	3.62	0	Ionic (Ligand Cationic)	false
N1	OH	TYR- 271	3.1	154.01	H-Bond (Ligand Donor)	false
C19	CG	GLU- 411	4.26	0	Hydrophobic	false
O22	O	GLU- 411	3.26	169.22	H-Bond (Ligand Donor)	false
C3	CB	ASN- 414	4.38	0	Hydrophobic	false
C5	CB	ASN- 414	4.49	0	Hydrophobic	false
C16	CB	ASN- 414	4.28	0	Hydrophobic	false
C3	CE1	PHE- 416	3.61	0	Hydrophobic	false
N1	OE2	GLU- 418	3.65	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 418	2.66	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 418	2.66	172.83	H-Bond (Ligand Donor)	false
C21	CD	ARG- 470	3.8	0	Hydrophobic	false
N29	O	HOH- 870	3.04	170.62	H-Bond (Protein Donor)	false
N26	O	HOH- 926	3.32	179.96	H-Bond (Protein Donor)	false
O20	MG	MG- 1300	2.72	0	Metal Acceptor	false