scPDB - 3q9o entry

Protein Data Bank Entry:

PDB ID : 3q9o

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2011-01-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cholix toxin
ID:	CHXA_VIBCL
AC:	Q5EK40
Organism:	Vibrio cholerae
Reign:	Bacteria
TaxID:	666
EC Number:	2.4.2.36

Chains:

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

Ligand binding site composition:

B-Factor:	22.372
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.283	1134.000

% Hydrophobic	% Polar
49.40	50.60
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	60.97 %
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
30.4848	29.5494	90.8281

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
N3A	NE2	GLN- 356	3.38	166.39	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 460	2.75	170.57	H-Bond (Ligand Donor)	false
O7N	N	GLY- 461	2.74	171.36	H-Bond (Protein Donor)	false
N7N	O	GLY- 461	3.06	156	H-Bond (Ligand Donor)	false
C2B	CB	THR- 462	4.36	0	Hydrophobic	false
O2B	OG1	THR- 462	2.63	157.54	H-Bond (Protein Donor)	false
C1B	CB	ALA- 466	4.13	0	Hydrophobic	false
C1B	CG2	VAL- 477	4.34	0	Hydrophobic	false
O3D	NH1	ARG- 479	2.98	168.07	H-Bond (Protein Donor)	false
C2D	CD2	TYR- 493	3.41	0	Hydrophobic	false
C5N	CB	TYR- 493	3.79	0	Hydrophobic	false
C5N	CB	ALA- 495	3.95	0	Hydrophobic	false
C5N	CG1	VAL- 500	4.24	0	Hydrophobic	false
C4D	CE1	TYR- 504	4.02	0	Hydrophobic	false
O2D	OE2	GLU- 581	2.75	137.42	H-Bond (Ligand Donor)	false
C5N	CB	GLU- 581	3.83	0	Hydrophobic	false
N1A	O	HOH- 987	2.79	179.96	H-Bond (Protein Donor)	false