scPDB - 4tsr entry

Protein Data Bank Entry:

PDB ID : 4tsr

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2014-06-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Periplasmic AppA protein
ID:	PPA_ECOLI
AC:	P07102
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.1.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	15.794
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.023	739.125

% Hydrophobic	% Polar
33.79	66.21
According to VolSite

Ligand :

HET Code:	IHS
Formula:	C6H6O24S6
Molecular weight:	654.487 g/mol
DrugBank ID:	DB01666
Buried Surface Area:	50.51 %
Polar Surface area:	448.86 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	0
Rings:	1
Aromatic rings:	0
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
-6.79011	-12.5146	-25.8156

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
O26	NH2	ARG- 16	3.29	162.97	H-Bond (Protein Donor)	false
O36	NE	ARG- 16	3.42	148.2	H-Bond (Protein Donor)	false
O26	CZ	ARG- 20	3.47	0	Ionic (Protein Cationic)	false
O26	NH1	ARG- 20	3.24	132.33	H-Bond (Protein Donor)	false
O26	NE	ARG- 20	2.89	150.44	H-Bond (Protein Donor)	false
O35	NH1	ARG- 20	3.44	135.52	H-Bond (Protein Donor)	false
O32	OG1	THR- 23	3.37	138.22	H-Bond (Protein Donor)	false
O23	NZ	LYS- 24	2.78	154.76	H-Bond (Protein Donor)	false
O23	NZ	LYS- 24	2.78	0	Ionic (Protein Cationic)	false
O32	NZ	LYS- 24	3.62	0	Ionic (Protein Cationic)	false
O46	NH2	ARG- 92	2.67	143.12	H-Bond (Protein Donor)	false
O46	NE	ARG- 92	2.87	135.88	H-Bond (Protein Donor)	false
O46	CZ	ARG- 92	3.17	0	Ionic (Protein Cationic)	false
O36	ND1	HIS- 303	3.45	141.67	H-Bond (Protein Donor)	false
O46	ND1	HIS- 303	2.7	147.32	H-Bond (Protein Donor)	false
O16	OD2	ASP- 304	3.18	138.05	H-Bond (Protein Donor)	false
O36	N	ASP- 304	2.94	166.45	H-Bond (Protein Donor)	false