scPDB - 3ko5 entry

Protein Data Bank Entry:

PDB ID : 3ko5

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2009-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-tyrosyl-tRNA(Tyr) deacylase
ID:	Q8IIS0_PLAF7
AC:	Q8IIS0
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	29.503
Number of residues:	14
Including
Standard Amino Acids:	14
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.716	509.625

% Hydrophobic	% Polar
51.66	48.34
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	31.91 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-11.3419	-14.746	-9.18711

Binding mode :

What is Poseview ?

2D View
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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
O3'	OG1	THR- 71	3.41	152.19	H-Bond (Protein Donor)	false
O2'	NE1	TRP- 72	3.04	173.65	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 89	4.3	0	Hydrophobic	false
DuAr	DuAr	PHE- 89	3.9	0	Aromatic Face/Face	false
C2'	CD2	PHE- 103	4.16	0	Hydrophobic	false
O3B	NE2	HIS- 104	2.91	137	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 104	2.98	149.11	H-Bond (Protein Donor)	false
N6	O	LYS- 107	3.03	140.75	H-Bond (Ligand Donor)	false