scPDB - 1e0j entry

Protein Data Bank Entry:

PDB ID : 1e0j

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2000-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA primase/helicase
ID:	PRIM_BPT7
AC:	P03692
Organism:	Enterobacteria phage T7
Reign:	Viruses
TaxID:	10760
EC Number:	2.7.7

Chains:

Chain Name:	Percentage of Residues within binding site
E	80 %
F	20 %

Ligand binding site composition:

B-Factor:	56.417
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.082	803.250

% Hydrophobic	% Polar
33.19	66.81
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	68.79 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
41.9035	37.3733	171.535

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
O1G	OG	SER- 314	3.37	171.21	H-Bond (Protein Donor)	false
O1G	N	GLY- 315	2.55	173.47	H-Bond (Protein Donor)	false
O2B	N	GLY- 317	3.31	176.31	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 318	2.74	169.75	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 318	2.74	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 318	3.59	0	Ionic (Protein Cationic)	false
O1B	N	SER- 319	3.11	149.37	H-Bond (Protein Donor)	false
O1A	N	THR- 320	2.96	161.82	H-Bond (Protein Donor)	false
O1A	OG1	THR- 320	3.27	148.69	H-Bond (Protein Donor)	false
C2'	CB	THR- 320	4.34	0	Hydrophobic	false
O2'	OG1	THR- 320	3.47	123.65	H-Bond (Ligand Donor)	false
DuAr	CZ	ARG- 504	3.71	24.28	Pi/Cation	false
N6	O	ASN- 512	3.39	146.89	H-Bond (Ligand Donor)	false
O3G	CZ	ARG- 522	2.74	0	Ionic (Protein Cationic)	false
O3'	O	PHE- 523	3	150.89	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 535	3.77	0	Aromatic Face/Face	false
C1'	CZ	TYR- 535	3.99	0	Hydrophobic	false
O2G	MG	MG- 701	2.61	0	Metal Acceptor	false
O1B	MG	MG- 701	2.7	0	Metal Acceptor	false