scPDB - 4gt8 entry

Protein Data Bank Entry:

PDB ID : 4gt8

Resolution :1.510 Å

Experimental Method : X-ray

Deposition Date : 2012-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sensor protein VraS
ID:	VRAS_STAAM
AC:	Q7A2Q0
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	158878
EC Number:	2.7.13.3

Chains:

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

Ligand binding site composition:

B-Factor:	25.291
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.539	317.250

% Hydrophobic	% Polar
57.45	42.55
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	64.73 %
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
13.8946	26.7044	36.4305

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
O2A	ND2	ASN- 263	2.83	124.33	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 267	2.94	171.5	H-Bond (Protein Donor)	false
C2'	CB	HIS- 267	4.07	0	Hydrophobic	false
N6	OD2	ASP- 290	2.91	164.32	H-Bond (Ligand Donor)	false
C1'	CD2	PHE- 295	3.71	0	Hydrophobic	false
C5'	CB	LYS- 300	4.33	0	Hydrophobic	false
C4'	CG	LYS- 300	4.04	0	Hydrophobic	false
C1'	CG	LYS- 300	4.5	0	Hydrophobic	false
C5'	CB	SER- 304	3.66	0	Hydrophobic	false
O1A	N	LEU- 307	3.07	149.16	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 307	4.2	0	Hydrophobic	false
O3B	MG	MG- 402	2.07	0	Metal Acceptor	false
O2A	MG	MG- 402	1.95	0	Metal Acceptor	false
N1	O	HOH- 502	2.77	156.11	H-Bond (Protein Donor)	false