scPDB - 3dge entry

Protein Data Bank Entry:

PDB ID : 3dge

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2008-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sensor histidine kinase
ID:	Q9WZV7_THEMA
AC:	Q9WZV7
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	77.294
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.197	1400.625

% Hydrophobic	% Polar
45.30	54.70
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	76.6 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
48.3445	70.6879	1.99622

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
O1A	ND2	ASN- 380	3.01	129.65	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 383	3.17	158.47	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 383	3.17	0	Ionic (Protein Cationic)	false
O2B	OH	TYR- 384	3.36	136.59	H-Bond (Protein Donor)	false
C2'	CZ	TYR- 384	3.37	0	Hydrophobic	false
N6	OD2	ASP- 411	2.87	143.36	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 424	4.45	0	Hydrophobic	false
O2B	NE	ARG- 430	2.9	144.8	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 430	3.68	0	Ionic (Protein Cationic)	false
C3'	CB	ARG- 430	4.48	0	Hydrophobic	false
O3'	N	VAL- 431	2.88	154.89	H-Bond (Protein Donor)	false
O2'	N	VAL- 431	3.31	132.21	H-Bond (Protein Donor)	false
C2'	CB	VAL- 431	4.19	0	Hydrophobic	false
C1'	CG2	VAL- 431	4.45	0	Hydrophobic	false
O1B	N	THR- 442	3.23	153.51	H-Bond (Protein Donor)	false
O1B	N	GLY- 443	2.75	153.39	H-Bond (Protein Donor)	false
O2A	N	LEU- 446	2.86	174.73	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 446	4.2	0	Hydrophobic	false