scPDB - 3lga entry

Protein Data Bank Entry:

PDB ID : 3lga

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2010-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI
ID:	TRMI_PYRAB
AC:	Q9V1J7
Organism:	Pyrococcus abyssi
Reign:	Archaea
TaxID:	272844
EC Number:	2.1.1.219

Chains:

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

Ligand binding site composition:

B-Factor:	30.785
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.858	570.375

% Hydrophobic	% Polar
49.11	50.89
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	76.93 %
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
-11.8867	21.096	29.7056

Binding mode :

What is Poseview ?

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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
O	N	VAL- 77	2.81	176.44	H-Bond (Protein Donor)	false
OXT	N	SER- 104	3.29	127.72	H-Bond (Protein Donor)	false
OXT	N	ALA- 106	3.09	148.92	H-Bond (Protein Donor)	false
O	N	LEU- 107	3.1	152.54	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 125	2.74	155.42	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 125	3.25	121.55	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 125	2.54	152.45	H-Bond (Ligand Donor)	false
C3'	CD1	PHE- 130	4.08	0	Hydrophobic	false
N6	OD2	ASP- 153	2.76	138.23	H-Bond (Ligand Donor)	false
N1	N	ILE- 154	3.13	165.21	H-Bond (Protein Donor)	false
N	OD2	ASP- 169	2.92	162.4	H-Bond (Ligand Donor)	false
N	OD2	ASP- 169	2.92	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 169	4.24	0	Hydrophobic	false
C1'	CD2	LEU- 170	4.29	0	Hydrophobic	false
N	O	HOH- 282	2.66	169.39	H-Bond (Ligand Donor)	false