scPDB - 1z0s entry

Protein Data Bank Entry:

PDB ID : 1z0s

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2005-03-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD kinase
ID:	NADK_ARCFU
AC:	O30297
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	65 %
C	35 %

Ligand binding site composition:

B-Factor:	12.269
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.006	786.375

% Hydrophobic	% Polar
41.63	58.37
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	62.44 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
9.79635	18.5733	-0.401032

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
C5'	CD1	LEU- 53	4	0	Hydrophobic	false
O1G	NH1	ARG- 54	3.07	124.48	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 54	3.22	131.2	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 54	3.91	0	Ionic (Protein Cationic)	false
O3'	ND2	ASN- 115	3.32	174.57	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 116	2.76	168.35	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 116	3.47	126.98	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 116	3.46	144.55	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 116	2.55	146.15	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 126	3.7	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 126	2.87	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 126	3.44	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 126	2.87	156.07	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 143	3.38	132.23	H-Bond (Protein Donor)	false
N6	OD2	ASP- 145	3.01	140.51	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 145	2.85	150.11	H-Bond (Ligand Donor)	false
C2'	CB	TYR- 158	3.82	0	Hydrophobic	false
O2'	N	TYR- 158	2.98	153.41	H-Bond (Protein Donor)	false
N7	OG	SER- 161	2.86	167.06	H-Bond (Protein Donor)	false
O1A	NE2	GLN- 211	2.87	156.91	H-Bond (Protein Donor)	false
O1B	MG	MG- 5002	2.52	0	Metal Acceptor	false
O3B	MG	MG- 5002	2.71	0	Metal Acceptor	false
O2A	MG	MG- 5002	1.93	0	Metal Acceptor	false