scPDB - 2yj4 entry

Protein Data Bank Entry:

PDB ID : 2yj4

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2011-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Copper-transporting ATPase
ID:	Q97UU7_SULSO
AC:	Q97UU7
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.639
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.980	691.875

% Hydrophobic	% Polar
49.76	50.24
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	75.41 %
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
-0.028129	-1.04471	25.6691

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
O3G	N	THR- 418	2.81	169.38	H-Bond (Protein Donor)	false
N6	OE1	GLU- 445	2.93	162.1	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 445	3.43	135.73	H-Bond (Ligand Donor)	false
O1B	NE2	HIS- 450	3.33	129.84	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 450	2.91	146.62	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 452	3.37	0	Hydrophobic	false
C1'	CB	LYS- 494	3.98	0	Hydrophobic	false
C2'	CD1	ILE- 501	3.98	0	Hydrophobic	false
O3G	OG	SER- 541	2.83	154.04	H-Bond (Protein Donor)	false
O2G	N	GLY- 542	2.76	150.33	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 569	3.96	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 569	2.62	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 569	2.62	161.49	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 591	3.14	125.73	H-Bond (Protein Donor)	false