scPDB - 3a25 entry

Protein Data Bank Entry:

PDB ID : 3a25

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-04-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase
ID:	TYW2_PYRHO
AC:	O58523
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	61.442
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.105	718.875

% Hydrophobic	% Polar
54.93	45.07
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	66.56 %
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
-2.43696	-29.9866	-35.511

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
CG	CG	MET- 107	3.98	0	Hydrophobic	false
O	N	SER- 109	3.1	165.06	H-Bond (Protein Donor)	false
C4'	CB	PHE- 133	4.42	0	Hydrophobic	false
C1'	CD1	PHE- 133	4.39	0	Hydrophobic	false
O3'	OE1	GLU- 155	2.78	167.89	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 155	3.24	157.35	H-Bond (Ligand Donor)	false
N3	N	LYS- 156	3.2	145.36	H-Bond (Protein Donor)	false
N6	OD1	ASP- 183	3.18	168.01	H-Bond (Ligand Donor)	false
N1	N	ASN- 184	2.94	152.81	H-Bond (Protein Donor)	false
C5'	CD1	TYR- 200	4.16	0	Hydrophobic	false