scPDB - 2xvm entry

Protein Data Bank Entry:

PDB ID : 2xvm

Resolution :1.480 Å

Experimental Method : X-ray

Deposition Date : 2010-10-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tellurite methyltransferase
ID:	TEHB_ECOLI
AC:	P25397
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.1.265

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	20.145
Number of residues:	37
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.991	1228.500

% Hydrophobic	% Polar
42.03	57.97
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	67.6 %
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
-35.902	-20.8045	-6.92823

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- 38	2.75	151.73	H-Bond (Ligand Donor)	false
O	NH2	ARG- 43	3.07	144.48	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 43	3.27	135.4	H-Bond (Protein Donor)	false
OXT	NE	ARG- 43	2.81	158.05	H-Bond (Protein Donor)	false
O	CZ	ARG- 43	3.75	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 43	3.51	0	Ionic (Protein Cationic)	false
O3'	OD2	ASP- 59	2.7	161.61	H-Bond (Ligand Donor)	false
O2'	NZ	LYS- 60	3.26	154.68	H-Bond (Protein Donor)	false
N3	N	LYS- 60	3.17	149.95	H-Bond (Protein Donor)	false
N6	OD1	ASP- 86	2.97	158.7	H-Bond (Ligand Donor)	false
N1	N	LEU- 87	2.93	168.59	H-Bond (Protein Donor)	false
N	O	THR- 102	2.77	159.25	H-Bond (Ligand Donor)	false
N	OG1	THR- 102	3.23	126.42	H-Bond (Ligand Donor)	false
O	OG1	THR- 102	2.83	158.66	H-Bond (Protein Donor)	false
CG	CG2	VAL- 103	3.95	0	Hydrophobic	false
CG	CG2	VAL- 104	4.01	0	Hydrophobic	false
C4'	CG2	VAL- 104	4.05	0	Hydrophobic	false
C5'	CE2	PHE- 107	3.68	0	Hydrophobic	false
N	O	HOH- 2048	2.92	156.19	H-Bond (Ligand Donor)	false