scPDB - 3pl9 entry

Protein Data Bank Entry:

PDB ID : 3pl9

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chlorophyll a-b binding protein, chloroplastic
ID:	F2Z293_SPIOL
AC:	F2Z293
Organism:	Spinacia oleracea
Reign:	Eukaryota
TaxID:	3562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.615
Number of residues:	43
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	7
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.581	273.375

% Hydrophobic	% Polar
55.56	44.44
According to VolSite

Ligand :

HET Code:	LUT
Formula:	C40H56O2
Molecular weight:	568.871 g/mol
DrugBank ID:	DB00137
Buried Surface Area:	43.05 %
Polar Surface area:	40.46 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
30.4754	1.73802	10.1726

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
C40	CB	MET- 104	4.27	0	Hydrophobic	false
C40	CD2	LEU- 105	4.36	0	Hydrophobic	false
C40	CD1	LEU- 108	3.55	0	Hydrophobic	false
C17	CD2	LEU- 111	4.11	0	Hydrophobic	false
O23	OD1	ASP- 179	2.75	124.19	H-Bond (Ligand Donor)	false
C22	CG	LEU- 181	3.55	0	Hydrophobic	false
C21	CD1	LEU- 181	4.19	0	Hydrophobic	false
O23	N	GLY- 182	3.5	127.94	H-Bond (Protein Donor)	false
C37	CD1	LEU- 183	3.64	0	Hydrophobic	false
C20	CB	HIS- 200	4.24	0	Hydrophobic	false
C19	CD1	LEU- 203	4.02	0	Hydrophobic	false
C20	CD2	LEU- 203	3.82	0	Hydrophobic	false
C20	CB	ALA- 204	4.23	0	Hydrophobic	false
C4	CE2	PHE- 211	3.7	0	Hydrophobic	false
C18	CD2	PHE- 211	3.56	0	Hydrophobic	false
C17	CE2	PHE- 211	3.77	0	Hydrophobic	false
O3	NE2	GLN- 214	3.07	133.42	H-Bond (Protein Donor)	false
O3	O	PRO- 222	2.98	120.08	H-Bond (Ligand Donor)	false
C1	CD2	TRP- 226	4.33	0	Hydrophobic	false
C2	CB	TRP- 226	3.86	0	Hydrophobic	false
C16	CE2	TRP- 226	3.86	0	Hydrophobic	false
C17	CE3	TRP- 226	3.61	0	Hydrophobic	false