scPDB - 1rg9 entry

Protein Data Bank Entry:

PDB ID : 1rg9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-adenosylmethionine synthase
ID:	METK_ECOLI
AC:	P0A817
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.5.1.6

Chains:

Chain Name:	Percentage of Residues within binding site
C	48 %
D	52 %

Ligand binding site composition:

B-Factor:	16.561
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:
Metals:	MG K MG

Cavity properties

Ligandability	Volume (Å3)
0.202	448.875

% Hydrophobic	% Polar
51.13	48.87
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	71.87 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-38.6933	28.3501	-4.77807

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
N	OE2	GLU- 55	3.02	0	Ionic (Ligand Cationic)	false
O	NE2	GLN- 98	2.91	161.81	H-Bond (Protein Donor)	false
OXT	NE2	GLN- 98	3.44	140.32	H-Bond (Protein Donor)	false
CB	CD1	ILE- 102	4.03	0	Hydrophobic	false
SD	CD1	ILE- 102	3.65	0	Hydrophobic	false
CE	CB	ASP- 118	3.62	0	Hydrophobic	false
O2'	OD1	ASP- 163	2.63	148.01	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 163	3.11	139.45	H-Bond (Ligand Donor)	false
C4'	CD	LYS- 165	3.6	0	Hydrophobic	false
N6	O	ARG- 229	2.8	129.48	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 230	3.65	0	Aromatic Face/Face	false
C1'	CZ	PHE- 230	3.77	0	Hydrophobic	false
N	OD1	ASP- 238	2.98	140.77	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 238	2.97	157.99	H-Bond (Ligand Donor)	false
N	OD1	ASP- 238	2.98	0	Ionic (Ligand Cationic)	false
C3'	CB	ASP- 238	3.68	0	Hydrophobic	false
C5'	CB	ASP- 238	4.33	0	Hydrophobic	false
O	NZ	LYS- 269	2.97	149.33	H-Bond (Protein Donor)	false
O	NZ	LYS- 269	2.97	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 269	3.88	0	Ionic (Protein Cationic)	false
CE	CD1	ILE- 302	3.6	0	Hydrophobic	false
OXT	O	HOH- 902	2.97	179.98	H-Bond (Protein Donor)	false