scPDB - 3aej entry

Protein Data Bank Entry:

PDB ID : 3aej

Resolution :2.590 Å

Experimental Method : X-ray

Deposition Date : 2010-02-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine gamma-lyase
ID:	Q86D28_ENTHI
AC:	Q86D28
Organism:	Entamoeba histolytica
Reign:	Eukaryota
TaxID:	5759
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	83 %
C	17 %

Ligand binding site composition:

B-Factor:	26.068
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.748	411.750

% Hydrophobic	% Polar
59.84	40.16
According to VolSite

Ligand :

HET Code:	AA5
Formula:	C13H16N2O7PS
Molecular weight:	375.314 g/mol
DrugBank ID:	-
Buried Surface Area:	81.56 %
Polar Surface area:	193.14 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
33.1929	3.79196	18.8965

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
O3P	N	GLY- 583	2.76	162.05	H-Bond (Protein Donor)	false
C5A	SD	MET- 584	4.08	0	Hydrophobic	false
O2P	N	MET- 584	2.96	157.08	H-Bond (Protein Donor)	false
SD	CZ	TYR- 608	3.86	0	Hydrophobic	false
CE	CE1	TYR- 608	3.94	0	Hydrophobic	false
C2A	CB	TYR- 608	4.16	0	Hydrophobic	false
C5A	CE2	TYR- 608	3.58	0	Hydrophobic	false
CB	CE1	TYR- 608	3.27	0	Hydrophobic	false
O2	ND2	ASN- 655	3.16	142.55	H-Bond (Protein Donor)	false
O3	ND2	ASN- 655	2.7	135.63	H-Bond (Protein Donor)	false
C2A	CB	ASN- 655	4.49	0	Hydrophobic	false
N1	OD2	ASP- 680	3.01	152.64	H-Bond (Protein Donor)	false
C2A	CB	THR- 682	3.75	0	Hydrophobic	false
C5A	CB	SER- 702	4.14	0	Hydrophobic	false
O4P	OG	SER- 702	2.7	164.4	H-Bond (Protein Donor)	false
O3P	OG	SER- 704	2.61	148.69	H-Bond (Protein Donor)	false
CG	CB	VAL- 831	3.94	0	Hydrophobic	false
SD	CG2	VAL- 831	4.38	0	Hydrophobic	false
O1	N	SER- 832	2.77	135.56	H-Bond (Protein Donor)	false
CG	CG2	THR- 847	3.94	0	Hydrophobic	false
CE	CG2	THR- 847	3.85	0	Hydrophobic	false
O1	NH2	ARG- 867	2.72	165.28	H-Bond (Protein Donor)	false
O1	NH1	ARG- 867	3.41	128.61	H-Bond (Protein Donor)	false
O2	NH1	ARG- 867	3	166.89	H-Bond (Protein Donor)	false
O1	CZ	ARG- 867	3.5	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 867	3.86	0	Ionic (Protein Cationic)	false
CE	CE2	PHE- 1044	3.73	0	Hydrophobic	false
CB	CZ	TYR- 1053	4.37	0	Hydrophobic	false
SD	CD2	TYR- 1053	4.17	0	Hydrophobic	false
O1P	OH	TYR- 1053	2.69	137.43	H-Bond (Protein Donor)	false
O1P	NE	ARG- 1055	3.25	139.69	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 1055	2.87	156.86	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 1055	3.5	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 1055	3.5	0	Ionic (Protein Cationic)	false