scPDB - 1j7k entry

Protein Data Bank Entry:

PDB ID : 1j7k

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2001-05-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Holliday junction ATP-dependent DNA helicase RuvB
ID:	RUVB_THEMA
AC:	Q56313
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.067
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.594	506.250

% Hydrophobic	% Polar
49.33	50.67
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	74.34 %
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
61.8675	-24.375	-26.3364

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
O1B	NH2	ARG- 20	2.94	127.64	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 20	3.3	132.39	H-Bond (Protein Donor)	false
O1A	NE	ARG- 20	2.75	168.47	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 20	3.46	0	Ionic (Protein Cationic)	false
N6	O	GLU- 26	2.98	138.42	H-Bond (Ligand Donor)	false
C1'	CZ	PHE- 27	3.93	0	Hydrophobic	false
N7	N	ILE- 28	2.76	166.19	H-Bond (Protein Donor)	false
O1G	N	GLY- 61	2.78	160.1	H-Bond (Protein Donor)	false
O3'	O	GLY- 61	2.66	153.17	H-Bond (Ligand Donor)	false
O2G	N	LEU- 62	3.27	125.23	H-Bond (Protein Donor)	false
O2G	N	GLY- 63	3	127.09	H-Bond (Protein Donor)	false
O3B	N	GLY- 63	3.19	147.44	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 64	3.66	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 64	2.91	0	Ionic (Protein Cationic)	false
O2G	N	LYS- 64	2.75	159.82	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 64	2.91	155.83	H-Bond (Protein Donor)	false
O3G	N	THR- 65	2.83	154.45	H-Bond (Protein Donor)	false
O3G	OG1	THR- 65	2.63	153.97	H-Bond (Protein Donor)	false
O2B	OG1	THR- 66	2.86	152.59	H-Bond (Protein Donor)	false
O2B	N	THR- 66	2.8	147.06	H-Bond (Protein Donor)	false
O3'	OH	TYR- 180	3.45	122.77	H-Bond (Protein Donor)	false
O2'	OH	TYR- 180	3.3	123.69	H-Bond (Ligand Donor)	false
C1'	CZ	TYR- 180	4.25	0	Hydrophobic	false
C2'	CD1	ILE- 188	4.15	0	Hydrophobic	false
O1B	NH2	ARG- 217	2.86	135.65	H-Bond (Protein Donor)	false
O2A	NE	ARG- 217	2.82	175.18	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 217	3.64	0	Ionic (Protein Cationic)	false
C5'	CD1	ILE- 220	4.25	0	Hydrophobic	false
C2'	CD1	ILE- 220	4.27	0	Hydrophobic	false