scPDB - 2zwa entry

Protein Data Bank Entry:

PDB ID : 2zwa

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2008-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA wybutosine-synthesizing protein 4
ID:	TYW4_YEAST
AC:	Q08282
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.1.1.290

Chains:

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

Ligand binding site composition:

B-Factor:	23.266
Number of residues:	32
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.950	486.000

% Hydrophobic	% Polar
42.36	57.64
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.05 %
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
-29.6519	-24.5853	11.1235

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
O	NZ	LYS- 38	3.45	134.46	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 38	3.02	173.86	H-Bond (Protein Donor)	false
O	NZ	LYS- 38	3.45	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 38	3.02	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 88	2.79	155.94	H-Bond (Protein Donor)	false
O	CZ	ARG- 88	3.85	0	Ionic (Protein Cationic)	false
N	O	GLY- 115	3.06	164.82	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 146	2.79	167.57	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 146	3.49	131.3	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 146	2.67	153.91	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 147	4.33	0	Hydrophobic	false
DuAr	DuAr	TYR- 147	3.75	0	Aromatic Face/Face	false
N6	OD1	ASP- 196	3.25	146.84	H-Bond (Ligand Donor)	false
N1	N	LEU- 197	2.86	176.45	H-Bond (Protein Donor)	false
N	O	GLU- 224	2.96	159.24	H-Bond (Ligand Donor)	false
C5'	CB	SER- 226	4.07	0	Hydrophobic	false
C5'	CE1	TYR- 229	3.95	0	Hydrophobic	false
N	O	HOH- 888	2.73	148.21	H-Bond (Ligand Donor)	false