scPDB - 4xzj entry

Protein Data Bank Entry:

PDB ID : 4xzj

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative NAD(+)--arginine ADP-ribosyltransferase Vis
ID:	VIS_VIBS1
AC:	A3UNN4
Organism:	Vibrio splendidus
Reign:	Bacteria
TaxID:	314291
EC Number:	2.4.2.31

Chains:

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

Ligand binding site composition:

B-Factor:	19.723
Number of residues:	48
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.761	722.250

% Hydrophobic	% Polar
47.66	52.34
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	66.66 %
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
4.79818	37.54	4.90405

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
C2D	CB	SER- 68	4.47	0	Hydrophobic	false
C5B	CE1	TYR- 72	4.25	0	Hydrophobic	false
C5D	CE1	TYR- 72	3.62	0	Hydrophobic	false
C4D	CZ	TYR- 72	3.69	0	Hydrophobic	false
C3D	CE2	TYR- 72	3.6	0	Hydrophobic	false
O2A	ND2	ASN- 76	2.89	173.74	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 80	2.94	168.28	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 80	2.97	152.55	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 80	3.7	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 80	3.87	0	Ionic (Protein Cationic)	false
O1A	CZ	ARG- 117	3.73	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 117	3.72	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 117	2.79	157.93	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 117	2.75	148.81	H-Bond (Protein Donor)	false
O7N	N	GLY- 118	2.96	162.06	H-Bond (Protein Donor)	false
N7N	O	GLY- 118	3.04	154.05	H-Bond (Ligand Donor)	false
C5D	CB	SER- 142	4.3	0	Hydrophobic	false
C2D	CB	SER- 142	4.49	0	Hydrophobic	false
C3N	CB	SER- 142	4.08	0	Hydrophobic	false
C5N	CB	SER- 144	4.02	0	Hydrophobic	false
C5N	CG1	VAL- 149	4.36	0	Hydrophobic	false
C4D	CE1	PHE- 153	3.94	0	Hydrophobic	false
C4B	CG	PRO- 158	4.45	0	Hydrophobic	false
O2D	OE1	GLU- 191	2.64	162.13	H-Bond (Ligand Donor)	false
C5N	CG	GLU- 191	4	0	Hydrophobic	false
O1A	O	HOH- 872	2.95	179.97	H-Bond (Protein Donor)	false
N6A	O	HOH- 895	3.23	168.38	H-Bond (Ligand Donor)	false