scPDB - 2ytz entry

Protein Data Bank Entry:

PDB ID : 2ytz

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2007-04-05

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))-dimethyltransferase
ID:	TRM1_PYRHO
AC:	O59493
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:	28.627
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.711	523.125

% Hydrophobic	% Polar
54.84	45.16
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	65.79 %
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
19.7541	130.686	13.6948

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
SD	CD2	PHE- 27	3.73	0	Hydrophobic	false
OXT	CZ	ARG- 36	3.55	0	Ionic (Protein Cationic)	false
OXT	NH1	ARG- 36	2.62	133.29	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 55	4.25	0	Hydrophobic	false
SD	CB	ALA- 57	4.15	0	Hydrophobic	false
C3'	CB	ALA- 57	4.36	0	Hydrophobic	false
CG	CB	ALA- 57	3.8	0	Hydrophobic	false
OXT	NE	ARG- 61	3.02	127.59	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 61	2.98	127.22	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 61	3.35	0	Ionic (Protein Cationic)	false
O3'	OD1	ASP- 78	2.66	163.61	H-Bond (Ligand Donor)	false
N3	N	ILE- 79	3.18	147.99	H-Bond (Protein Donor)	false
N6	OD1	ASP- 120	2.83	170.64	H-Bond (Ligand Donor)	false
N1	N	ALA- 121	2.81	169.95	H-Bond (Protein Donor)	false
SD	CZ	PHE- 140	3.49	0	Hydrophobic	false
C3'	CE2	PHE- 140	4.04	0	Hydrophobic	false
O	O	HOH- 1009	2.77	179.94	H-Bond (Protein Donor)	false