scPDB - 3amt entry

Protein Data Bank Entry:

PDB ID : 3amt

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2010-08-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
ID:	TIAS_ARCFU
AC:	O28025
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	6.3.4.22

Chains:

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

Ligand binding site composition:

B-Factor:	54.077
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.472	759.375

% Hydrophobic	% Polar
34.22	65.78
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	82.42 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.0792	90.5649	70.5818

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
O1B	OD2	ASP- 8	3.48	154.09	H-Bond (Protein Donor)	false
O2A	N	ASP- 9	3.19	135.16	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 9	3.43	151.62	H-Bond (Ligand Donor)	false
C3'	CB	ASP- 9	3.38	0	Hydrophobic	false
O1G	N	TPO- 18	3.29	146.5	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 49	4.38	0	Hydrophobic	false
C4'	CB	TYR- 51	3.97	0	Hydrophobic	false
C1'	CD1	TYR- 51	4.41	0	Hydrophobic	false
O2B	N	THR- 53	3.48	132.57	H-Bond (Protein Donor)	false
O1A	OG1	THR- 53	3.01	133.52	H-Bond (Protein Donor)	false
O3A	N	THR- 53	3.01	164.33	H-Bond (Protein Donor)	false
O2B	N	ARG- 54	3.13	133.2	H-Bond (Protein Donor)	false
O2B	N	GLY- 55	2.83	151.82	H-Bond (Protein Donor)	false
O2B	N	ASN- 56	2.66	144.1	H-Bond (Protein Donor)	false
N7	ND2	ASN- 56	3.45	149.41	H-Bond (Protein Donor)	false
O1B	N	GLY- 57	2.75	146.86	H-Bond (Protein Donor)	false
N6	O	ALA- 112	2.82	143.69	H-Bond (Ligand Donor)	false
N6	O	ASP- 115	3.29	139.2	H-Bond (Ligand Donor)	false
N1	N	LEU- 117	3.22	164.86	H-Bond (Protein Donor)	false
C1'	CG	ARG- 140	3.92	0	Hydrophobic	false
O2'	N	GLY- 144	3.16	166.51	H-Bond (Protein Donor)	false