scPDB - 1qs2 entry

Protein Data Bank Entry:

PDB ID : 1qs2

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1999-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vip2Ac
ID:	Q844J9_BACTU
AC:	Q844J9
Organism:	Bacillus thuringiensis
Reign:	Bacteria
TaxID:	1428
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.581
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.117	739.125

% Hydrophobic	% Polar
38.81	61.19
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	47.73 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
27.4803	4.30073	58.2827

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
C5D	CE1	TYR- 307	3.51	0	Hydrophobic	false
C4D	CZ	TYR- 307	4.14	0	Hydrophobic	false
DuAr	CZ	ARG- 315	3.69	160.71	Pi/Cation	false
O1N	CZ	ARG- 349	3.76	0	Ionic (Protein Cationic)	false
O7N	N	TRP- 350	2.57	161.97	H-Bond (Protein Donor)	false
N7N	O	TRP- 350	2.96	153.58	H-Bond (Ligand Donor)	false
C2D	CB	SER- 386	3.85	0	Hydrophobic	false
C5N	CB	SER- 386	4.48	0	Hydrophobic	false
C5N	CB	SER- 388	3.96	0	Hydrophobic	false
O1A	NH2	ARG- 400	3.35	130.08	H-Bond (Protein Donor)	false
O2D	OG	SER- 425	3.42	133.11	H-Bond (Protein Donor)	false
O2D	OE1	GLU- 428	2.81	131.29	H-Bond (Ligand Donor)	false
O2D	OE2	GLU- 428	3.2	166.25	H-Bond (Ligand Donor)	false
O2A	O	HOH- 1033	2.86	179.98	H-Bond (Protein Donor)	false