scPDB - 3ewk entry

Protein Data Bank Entry:

PDB ID : 3ewk

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2008-10-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sensory box histidine kinase/response regulator
ID:	Q609M8_METCA
AC:	Q609M8
Organism:	Methylococcus capsulatus
Reign:	Bacteria
TaxID:	243233
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	51.995
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.478	357.750

% Hydrophobic	% Polar
54.72	45.28
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	58.65 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
23.9158	-49.0403	-15.3742

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
C8M	CB	THR- 103	4.43	0	Hydrophobic	false
C7	CG2	THR- 103	3.93	0	Hydrophobic	false
C9A	CB	HIS- 132	3.96	0	Hydrophobic	false
C3'	CB	ARG- 133	3.69	0	Hydrophobic	false
O1P	CZ	ARG- 133	3.72	0	Ionic (Protein Cationic)	false
C4'	CB	ASN- 136	4.1	0	Hydrophobic	false
O3B	O	LYS- 142	3.24	160.42	H-Bond (Ligand Donor)	false
O2P	NZ	LYS- 142	3.22	155.21	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 142	3.22	0	Ionic (Protein Cationic)	false
C2B	CG2	ILE- 145	3.84	0	Hydrophobic	false
C5'	CG1	ILE- 145	3.54	0	Hydrophobic	false
C2B	CB	ARG- 146	3.43	0	Hydrophobic	false
C1'	CE	MET- 148	3.84	0	Hydrophobic	false
C9	CE	MET- 148	3.62	0	Hydrophobic	false
C8M	CH2	TRP- 149	3.65	0	Hydrophobic	false
C1'	CZ2	TRP- 149	4.22	0	Hydrophobic	false
O2'	NE1	TRP- 149	3.12	157.1	H-Bond (Protein Donor)	false
C8M	CD1	ILE- 152	3.97	0	Hydrophobic	false
N3	OD1	ASN- 164	2.78	173.81	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 164	2.9	152.82	H-Bond (Protein Donor)	false
C7M	CG2	ILE- 178	3.79	0	Hydrophobic	false
C9A	CD1	ILE- 178	4.42	0	Hydrophobic	false
C6	CD1	ILE- 178	3.68	0	Hydrophobic	false
C7M	CB	TYR- 191	3.61	0	Hydrophobic	false
C8M	CD1	TYR- 191	3.64	0	Hydrophobic	false
C7M	CB	SER- 193	3.74	0	Hydrophobic	false