scPDB - 1gzf entry

Protein Data Bank Entry:

PDB ID : 1gzf

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2002-05-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mono-ADP-ribosyltransferase C3
ID:	ARC3_CBDP
AC:	P15879
Organism:	Clostridium botulinum D phage
Reign:	Viruses
TaxID:	29342
EC Number:	2.4.2

Chains:

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

Ligand binding site composition:

B-Factor:	36.984
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.371	2173.500

% Hydrophobic	% Polar
39.13	60.87
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	57.5 %
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
20.263	4.57193	2.5682

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
O3D	O	THR- 80	2.75	170.39	H-Bond (Ligand Donor)	false
C3D	CB	ALA- 83	3.81	0	Hydrophobic	false
C5B	CB	SER- 84	4.39	0	Hydrophobic	false
O2A	ND2	ASN- 87	2.8	157.47	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 128	3.38	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 128	3.69	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 128	2.85	125.73	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 128	3.33	131.05	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 128	3.27	132.82	H-Bond (Protein Donor)	false
O7N	N	GLY- 129	2.92	161.07	H-Bond (Protein Donor)	false
N7N	O	GLY- 129	3	171.21	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 130	2.71	160.32	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 131	2.79	131.12	H-Bond (Ligand Donor)	false
O2B	N	ASP- 131	2.83	161.29	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 169	2.85	129.45	H-Bond (Ligand Donor)	false
C2D	CB	SER- 174	4.24	0	Hydrophobic	false
C5N	CB	SER- 174	4.12	0	Hydrophobic	false
O2N	CZ	ARG- 186	3.78	0	Ionic (Protein Cationic)	false
O2N	NH1	ARG- 186	3.03	169.47	H-Bond (Protein Donor)	false
O2D	NE2	GLN- 212	3.3	135.12	H-Bond (Protein Donor)	false
C5N	CB	GLN- 212	4.33	0	Hydrophobic	false
O2D	OE1	GLU- 214	2.87	140.01	H-Bond (Ligand Donor)	false
C5N	CG	GLU- 214	3.88	0	Hydrophobic	false
O1A	O	HOH- 2164	2.7	179.97	H-Bond (Protein Donor)	false