scPDB - 3pb3 entry

Protein Data Bank Entry:

PDB ID : 3pb3

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-10-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	16S rRNA (adenine(1408)-N(1))-methyltransferase
ID:	NPMA_ECOLX
AC:	A8C927
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	2.1.1.180

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	16.581
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.776	1707.750

% Hydrophobic	% Polar
47.43	52.57
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	72.51 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
10.1083	8.67058	26.1403

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	O	GLY- 32	2.78	154.67	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 55	2.71	168.51	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 55	3.27	120.79	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 55	2.63	156.25	H-Bond (Ligand Donor)	false
N1	N	ALA- 87	2.78	175.62	H-Bond (Protein Donor)	false
N6	OE1	GLU- 88	2.99	145.77	H-Bond (Ligand Donor)	false
N	O	LEU- 104	2.68	160.86	H-Bond (Ligand Donor)	false
C5'	CB	TRP- 107	3.93	0	Hydrophobic	false
N6	OG1	THR- 109	3.13	168.67	H-Bond (Ligand Donor)	false
O	OG	SER- 195	2.61	155.47	H-Bond (Protein Donor)	false
CG	CB	TRP- 197	4.45	0	Hydrophobic	false
SD	CE2	TRP- 197	4.31	0	Hydrophobic	false
SD	CD	ARG- 200	4.21	0	Hydrophobic	false
C3'	CD	ARG- 200	4.42	0	Hydrophobic	false
N	O	HOH- 238	2.79	163.6	H-Bond (Ligand Donor)	false