scPDB - 1yid entry

Protein Data Bank Entry:

PDB ID : 1yid

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2005-01-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan--tRNA ligase 2
ID:	SYW2_DEIRA
AC:	Q9RVD6
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	6.1.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	67.596
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.753	1582.875

% Hydrophobic	% Polar
32.62	67.38
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	49.87 %
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
72.597	-14.5352	2.46861

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
O3'	O	GLY- 28	3.04	163.01	H-Bond (Ligand Donor)	false
C4'	CB	ASP- 29	3.93	0	Hydrophobic	false
O1G	NH1	ARG- 30	3.06	144.41	H-Bond (Protein Donor)	false
O2A	NE	ARG- 30	3.43	151.36	H-Bond (Protein Donor)	false
N6	O	LEU- 207	3.06	156.56	H-Bond (Ligand Donor)	false
O2B	OG	SER- 217	3.33	128.35	H-Bond (Protein Donor)	false
O3B	OG	SER- 217	3.05	155.96	H-Bond (Protein Donor)	false
O3G	OG	SER- 219	2.79	161.41	H-Bond (Protein Donor)	false
O1B	MG	MG- 3001	2.32	0	Metal Acceptor	false
O1A	MG	MG- 3001	2.44	0	Metal Acceptor	false