scPDB - 3rfa entry

Protein Data Bank Entry:

PDB ID : 3rfa

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2011-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dual-specificity RNA methyltransferase RlmN
ID:	RLMN_ECOLI
AC:	P36979
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.449
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.609	1879.875

% Hydrophobic	% Polar
29.62	70.38
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	67.23 %
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
-17.5619	-1.55344	-13.5021

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
C2'	CE1	PHE- 131	3.86	0	Hydrophobic	false
C5'	CB	MET- 176	3.88	0	Hydrophobic	false
C4'	CE	MET- 176	4.19	0	Hydrophobic	false
N	O	GLY- 179	3.01	163.8	H-Bond (Ligand Donor)	false
N	OE1	GLU- 180	3.19	151.73	H-Bond (Ligand Donor)	false
OXT	OG	SER- 211	2.58	151.18	H-Bond (Protein Donor)	false
CB	CB	SER- 211	4.11	0	Hydrophobic	false
O	OG	SER- 233	3.06	155.47	H-Bond (Protein Donor)	false
OXT	OG	SER- 233	2.51	137.27	H-Bond (Protein Donor)	false
C3'	CB	SER- 233	4.19	0	Hydrophobic	false
C1'	CG2	VAL- 280	4.36	0	Hydrophobic	false
N6	O	ASN- 312	3.03	160.98	H-Bond (Ligand Donor)	false
N1	N	ASN- 312	3.11	171.25	H-Bond (Protein Donor)	false
O3'	O	HOH- 446	2.88	179.96	H-Bond (Protein Donor)	false