scPDB - 3to3 entry

Protein Data Bank Entry:

PDB ID : 3to3

Resolution :2.380 Å

Experimental Method : X-ray

Deposition Date : 2011-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Petrobactin biosynthesis protein AsbB
ID:	Q81RQ8_BACAN
AC:	Q81RQ8
Organism:	Bacillus anthracis
Reign:	Bacteria
TaxID:	1392
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	58.759
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.478	840.375

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	60.95 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-1.76304	-27.767	31.8765

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
O1B	OG	SER- 280	2.83	153.38	H-Bond (Protein Donor)	false
C5'	CB	SER- 280	4.12	0	Hydrophobic	false
O1B	NH2	ARG- 282	3.5	129.13	H-Bond (Protein Donor)	false
O1B	NE	ARG- 282	2.94	152.1	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 282	3.06	143.13	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 282	3.34	132.15	H-Bond (Protein Donor)	false
O1A	NE	ARG- 282	3.49	130.02	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 282	3.63	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 282	3.99	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 282	3.8	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 296	2.83	162.74	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 308	2.62	143.04	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 308	3.69	0	Ionic (Protein Cationic)	false
N6	OH	TYR- 388	3.14	138.86	H-Bond (Ligand Donor)	false
O2'	O	HOH- 646	2.73	163.73	H-Bond (Protein Donor)	false
N6	O	HOH- 663	3.4	165.09	H-Bond (Ligand Donor)	false