scPDB - 3sqx entry

Protein Data Bank Entry:

PDB ID : 3sqx

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2011-07-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent RNA helicase MSS116, mitochondrial
ID:	MS116_YEAST
AC:	P15424
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	3.6.4.13

Chains:

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

Ligand binding site composition:

B-Factor:	43.074
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.483	587.250

% Hydrophobic	% Polar
45.40	54.60
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	67.03 %
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
66.8725	33.7231	16.8412

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
C2'	CZ	PHE- 126	4.48	0	Hydrophobic	false
C1'	CE1	PHE- 126	4.36	0	Hydrophobic	false
DuAr	DuAr	PHE- 126	3.57	0	Aromatic Face/Face	false
N6	O	GLY- 128	2.78	167.68	H-Bond (Ligand Donor)	false
N7	NE2	GLN- 133	2.8	170.09	H-Bond (Protein Donor)	false
N6	OE1	GLN- 133	2.86	150.37	H-Bond (Ligand Donor)	false
O2B	N	THR- 156	3.46	132.54	H-Bond (Protein Donor)	false
O3A	N	GLY- 157	3.2	146.86	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 158	2.71	153.34	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 158	2.82	129.98	H-Bond (Protein Donor)	false
O2B	N	LYS- 158	2.98	166.09	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 158	2.71	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 158	2.82	0	Ionic (Protein Cationic)	false
O1A	N	THR- 159	2.99	155.62	H-Bond (Protein Donor)	false
O1A	OG1	THR- 159	2.68	156.2	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 441	2.58	170.15	H-Bond (Ligand Donor)	false
O3G	NH2	ARG- 466	2.73	147.15	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 466	2.95	136.02	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 466	3.26	0	Ionic (Protein Cationic)	false
O3G	NH1	ARG- 469	2.89	159.16	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 469	3.64	0	Ionic (Protein Cationic)	false
C4'	CB	SER- 470	4.06	0	Hydrophobic	false
C1'	CB	SER- 470	4.33	0	Hydrophobic	false
O4'	OG	SER- 470	3.49	143.46	H-Bond (Protein Donor)	false
O1G	MG	MG- 900	2	0	Metal Acceptor	false
O1B	MG	MG- 900	2.04	0	Metal Acceptor	false
O2G	O	HOH- 1006	2.99	179.99	H-Bond (Protein Donor)	false
O2'	O	HOH- 1050	2.72	162.25	H-Bond (Protein Donor)	false