scPDB - 2qjo entry

Protein Data Bank Entry:

PDB ID : 2qjo

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2007-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional NMN adenylyltransferase/Nudix hydrolase
ID:	NADM_SYNY3
AC:	Q55928
Organism:	Synechocystis sp.
Reign:	Bacteria
TaxID:	1111708
EC Number:	2.7.7.1

Chains:

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

Ligand binding site composition:

B-Factor:	35.254
Number of residues:	54
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.232	2517.750

% Hydrophobic	% Polar
43.30	56.70
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	71.57 %
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
-92.3801	16.7368	-22.441

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
C5B	CZ	TYR- 10	4.47	0	Hydrophobic	false
C4B	CE2	TYR- 10	3.59	0	Hydrophobic	false
O4B	OH	TYR- 10	2.68	138.59	H-Bond (Protein Donor)	false
C5D	CG2	ILE- 11	4.02	0	Hydrophobic	false
O1A	N	ARG- 13	3.08	137.13	H-Bond (Protein Donor)	false
O3	N	ARG- 13	3.19	154.48	H-Bond (Protein Donor)	false
C3D	CG	ARG- 13	3.66	0	Hydrophobic	false
O1A	N	PHE- 14	3.09	164.66	H-Bond (Protein Donor)	false
C5B	CE2	PHE- 14	4.24	0	Hydrophobic	false
O3D	OG	SER- 41	2.94	159.06	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 80	2.64	158.3	H-Bond (Ligand Donor)	false
O7N	N	TRP- 81	2.56	168.88	H-Bond (Protein Donor)	false
N7N	O	TRP- 81	2.95	152.67	H-Bond (Ligand Donor)	false
N7N	OD1	ASP- 85	2.73	165	H-Bond (Ligand Donor)	false
C3N	CB	TRP- 88	4.03	0	Hydrophobic	false
DuAr	DuAr	TRP- 88	3.83	0	Aromatic Face/Face	false
O3B	N	HIS- 111	3.3	169.8	H-Bond (Protein Donor)	false
C1B	CB	HIS- 111	4.48	0	Hydrophobic	false
O2N	OH	TYR- 119	2.52	159.14	H-Bond (Protein Donor)	false
C5D	CZ	TYR- 119	3.53	0	Hydrophobic	false
C5N	CB	TYR- 119	3.87	0	Hydrophobic	false
N6A	O	TYR- 134	2.91	175.01	H-Bond (Ligand Donor)	false
N1A	N	TYR- 134	2.78	164.91	H-Bond (Protein Donor)	false
N6A	O	PHE- 137	2.97	142.99	H-Bond (Ligand Donor)	false
O3B	O	HOH- 717	2.82	152.26	H-Bond (Ligand Donor)	false