scPDB - 4xbo entry

Protein Data Bank Entry:

PDB ID : 4xbo

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2014-12-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
ID:	TRMJ_ECOLI
AC:	P0AE01
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.1.200

Chains:

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

Ligand binding site composition:

B-Factor:	46.595
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.980	502.875

% Hydrophobic	% Polar
40.94	59.06
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	72.32 %
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
-31.7829	-26.3303	-4.04904

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'	CB	THR- 79	4.18	0	Hydrophobic	false
OXT	OG	SER- 80	3.24	164.18	H-Bond (Protein Donor)	false
O	N	ALA- 81	2.82	164.59	H-Bond (Protein Donor)	false
O2'	N	GLY- 114	3.33	151.97	H-Bond (Protein Donor)	false
N6	O	ILE- 134	3.2	152.1	H-Bond (Ligand Donor)	false
N1	N	ILE- 134	2.9	162.52	H-Bond (Protein Donor)	false
N6	O	SER- 141	3.03	147.01	H-Bond (Ligand Donor)	false
CB	CB	SER- 142	3.91	0	Hydrophobic	false
N7	N	LEU- 143	2.86	144.87	H-Bond (Protein Donor)	false
C5'	CB	LEU- 145	4.46	0	Hydrophobic	false
C4'	CD1	LEU- 145	4.09	0	Hydrophobic	false
C1'	CB	ALA- 148	3.66	0	Hydrophobic	false