scPDB - 3axt entry

Protein Data Bank Entry:

PDB ID : 3axt

Resolution :2.490 Å

Experimental Method : X-ray

Deposition Date : 2011-04-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
ID:	TRM1_AQUAE
AC:	O67010
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.744
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.419	428.625

% Hydrophobic	% Polar
50.39	49.61
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	60.7 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.1016	12.8034	45.7803

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	LEU- 60	2.73	162.1	H-Bond (Ligand Donor)	false
C1'	CD2	LEU- 60	4.12	0	Hydrophobic	false
C5'	CB	LEU- 60	3.89	0	Hydrophobic	false
C4'	CB	ALA- 62	4.44	0	Hydrophobic	false
CG	CB	ALA- 62	3.99	0	Hydrophobic	false
OXT	NE	ARG- 66	2.7	140.86	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 66	3.53	0	Ionic (Protein Cationic)	false
O3'	OD2	ASP- 84	3.41	155.06	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 84	3	167.87	H-Bond (Ligand Donor)	false
N3	N	ILE- 85	3.37	156.55	H-Bond (Protein Donor)	false
N6	OE2	GLU- 113	3.16	150.4	H-Bond (Ligand Donor)	false
N1	N	ALA- 114	2.81	168.98	H-Bond (Protein Donor)	false
N	OD2	ASP- 132	3.22	150.03	H-Bond (Ligand Donor)	false
N	OD2	ASP- 132	3.22	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 132	4.43	0	Hydrophobic	false
SD	CZ	PHE- 134	3.74	0	Hydrophobic	false
CE	CE1	PHE- 134	3.24	0	Hydrophobic	false
C5'	CE2	PHE- 134	4.28	0	Hydrophobic	false
C3'	CE2	PHE- 134	4.14	0	Hydrophobic	false
O	O	HOH- 398	2.71	156.45	H-Bond (Protein Donor)	false
O	O	HOH- 399	2.73	179.96	H-Bond (Protein Donor)	false
N	O	HOH- 403	3.42	127.44	H-Bond (Ligand Donor)	false