scPDB - 1mxi entry

Protein Data Bank Entry:

PDB ID : 1mxi

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2002-10-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (cytidine(34)-2'-O)-methyltransferase
ID:	TRML_HAEIN
AC:	P44868
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.902
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.743	276.750

% Hydrophobic	% Polar
40.24	59.76
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.57 %
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
1.57677	-15.7998	-2.05515

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	LEU- 78	4.36	0	Hydrophobic	false
O2'	O	LEU- 78	2.79	155.75	H-Bond (Ligand Donor)	false
C1'	CD2	PHE- 99	4.29	0	Hydrophobic	false
O3'	N	GLY- 100	3.16	122.82	H-Bond (Protein Donor)	false
O2'	N	GLY- 100	2.99	157.83	H-Bond (Protein Donor)	false
N6	O	ILE- 122	2.83	150.2	H-Bond (Ligand Donor)	false
N1	N	ILE- 122	2.73	172.8	H-Bond (Protein Donor)	false
CB	CB	SER- 130	4.09	0	Hydrophobic	false
C4'	CD1	LEU- 133	3.76	0	Hydrophobic	false
C1'	CB	SER- 136	3.8	0	Hydrophobic	false
N	O	HOH- 1001	3.15	162.4	H-Bond (Ligand Donor)	false
O3'	O	HOH- 1002	2.78	179.96	H-Bond (Protein Donor)	false