scPDB - 1rj9 entry

Protein Data Bank Entry:

PDB ID : 1rj9

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2003-11-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Signal recognition particle receptor FtsY
ID:	FTSY_THEAQ
AC:	P83749
Organism:	Thermus aquaticus
Reign:	Bacteria
TaxID:	271
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	80 %
B	20 %

Ligand binding site composition:

B-Factor:	14.113
Number of residues:	51
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	6
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.394	621.000

% Hydrophobic	% Polar
42.39	57.61
According to VolSite

Ligand :

HET Code:	GCP
Formula:	C11H14N5O13P3
Molecular weight:	517.176 g/mol
DrugBank ID:	DB03725
Buried Surface Area:	75.83 %
Polar Surface area:	326.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
32.6233	8.37244	29.1559

Binding mode :

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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
C1'	CB	GLN- 107	3.71	0	Hydrophobic	false
C4'	CB	GLN- 107	3.86	0	Hydrophobic	false
O3G	N	GLY- 112	2.92	160.61	H-Bond (Protein Donor)	false
O2B	N	GLY- 114	2.77	163.09	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 115	3.94	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 115	2.75	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 115	2.72	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 115	2.75	155.14	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 115	2.72	149.34	H-Bond (Protein Donor)	false
O2B	N	LYS- 115	2.93	158.92	H-Bond (Protein Donor)	false
O1B	N	THR- 116	3.02	174.01	H-Bond (Protein Donor)	false
O1A	N	THR- 117	2.73	160.02	H-Bond (Protein Donor)	false
O1A	OG1	THR- 117	2.71	154.36	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 138	3.59	0	Ionic (Protein Cationic)	false
O1G	NH1	ARG- 142	3	154.85	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 148	2.93	161.76	H-Bond (Protein Donor)	false
O6	N	LYS- 256	2.93	156.19	H-Bond (Protein Donor)	false
N1	OD2	ASP- 258	2.83	158.39	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 258	3.48	129.07	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 258	3.38	133.22	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 258	2.76	154.89	H-Bond (Ligand Donor)	false
O6	N	GLY- 283	3.23	158.62	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 284	2.57	149.79	H-Bond (Ligand Donor)	false
C1'	CG	GLU- 284	4.17	0	Hydrophobic	false
O2G	MG	MG- 501	2.33	0	Metal Acceptor	false
O1B	MG	MG- 501	2.25	0	Metal Acceptor	false
O2G	O	HOH- 713	2.67	179.95	H-Bond (Protein Donor)	false