scPDB - 3dnt entry

Protein Data Bank Entry:

PDB ID : 3dnt

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2008-07-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase toxin HipA
ID:	HIPA_ECOLI
AC:	P23874
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.475
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.491	425.250

% Hydrophobic	% Polar
56.35	43.65
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	74.77 %
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
-2.74529	8.68935	53.7075

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
C4'	CG2	VAL- 98	4.42	0	Hydrophobic	false
C2'	CG1	VAL- 98	4.4	0	Hydrophobic	false
C1'	CG2	VAL- 98	3.72	0	Hydrophobic	false
C5'	CG1	VAL- 151	4.1	0	Hydrophobic	false
C4'	CB	ALA- 152	4.38	0	Hydrophobic	false
O1B	N	GLN- 155	3.19	139.1	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 157	2.57	162.69	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 157	2.57	0	Ionic (Protein Cationic)	false
C1'	CD1	ILE- 179	4.18	0	Hydrophobic	false
O2B	NZ	LYS- 181	2.76	144.17	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 181	2.81	148.54	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 181	2.76	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 181	2.81	0	Ionic (Protein Cationic)	false
N6	O	GLU- 234	2.95	139.77	H-Bond (Ligand Donor)	false
N1	N	PHE- 236	2.88	157.85	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 236	3.71	0	Aromatic Face/Face	false
N3	NE2	GLN- 252	3.4	164.92	H-Bond (Protein Donor)	false
O1G	NE2	HIS- 311	2.98	154.26	H-Bond (Protein Donor)	false
O3'	O	LYS- 313	3.2	162.9	H-Bond (Ligand Donor)	false
C3'	CE1	TYR- 331	3.21	0	Hydrophobic	false
O1G	MG	MG- 441	2.63	0	Metal Acceptor	false
O3B	MG	MG- 441	2.31	0	Metal Acceptor	false
O2A	MG	MG- 441	2.32	0	Metal Acceptor	false
O2B	MG	MG- 442	2.79	0	Metal Acceptor	false
O2'	O	HOH- 861	2.7	179.95	H-Bond (Protein Donor)	false