scPDB - 2rd2 entry

Protein Data Bank Entry:

PDB ID : 2rd2

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2007-09-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamine--tRNA ligase
ID:	SYQ_ECOLI
AC:	P00962
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.18

Chains:

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

Ligand binding site composition:

B-Factor:	25.844
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.118	624.375

% Hydrophobic	% Polar
42.70	57.30
According to VolSite

Ligand :

HET Code:	QSI
Formula:	C15H22N8O8S
Molecular weight:	474.449 g/mol
DrugBank ID:	-
Buried Surface Area:	76.32 %
Polar Surface area:	272.95 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
42.1648	28.6877	16.186

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
C4'	CE1	PHE- 31	3.86	0	Hydrophobic	false
N	O	PRO- 32	3.4	159.84	H-Bond (Ligand Donor)	false
CB	CG	PRO- 32	3.88	0	Hydrophobic	false
C5'	CB	PRO- 33	4.13	0	Hydrophobic	false
O2S	N	GLU- 34	3.03	154.21	H-Bond (Protein Donor)	false
C1'	CB	SER- 46	3.95	0	Hydrophobic	false
N	OD2	ASP- 66	3.16	144.22	H-Bond (Ligand Donor)	false
N	OD2	ASP- 66	3.16	0	Ionic (Ligand Cationic)	false
OE1	OH	TYR- 211	3.08	138.09	H-Bond (Protein Donor)	false
CG	CE1	TYR- 211	3.5	0	Hydrophobic	false
O2'	N	THR- 230	3.15	126.33	H-Bond (Protein Donor)	false
O2'	OG1	THR- 230	2.71	154.04	H-Bond (Ligand Donor)	false
C2'	CG2	THR- 230	4.35	0	Hydrophobic	false
CG	CZ	PHE- 233	3.74	0	Hydrophobic	false
N1	N	LEU- 261	2.92	166.16	H-Bond (Protein Donor)	false
N6	O	LEU- 261	3.22	159.15	H-Bond (Ligand Donor)	false
O2S	NZ	LYS- 270	3.22	160.35	H-Bond (Protein Donor)	false