scPDB - 1vbm entry

Protein Data Bank Entry:

PDB ID : 1vbm

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2004-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine--tRNA ligase
ID:	SYY_ECOLI
AC:	P0AGJ9
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	41.168
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.566	749.250

% Hydrophobic	% Polar
40.09	59.91
According to VolSite

Ligand :

HET Code:	YSA
Formula:	C19H23N7O8S
Molecular weight:	509.493 g/mol
DrugBank ID:	DB03325
Buried Surface Area:	75.09 %
Polar Surface area:	250.09 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.5365	160.455	209.809

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
OH	OH	TYR- 37	2.73	141.73	H-Bond (Protein Donor)	false
C4'	CD1	PHE- 40	3.97	0	Hydrophobic	false
CB	CB	ASP- 41	4.23	0	Hydrophobic	false
C5'	CB	HIS- 51	4.23	0	Hydrophobic	false
C4'	CG	PRO- 54	4.29	0	Hydrophobic	false
C1'	CG	PRO- 54	3.4	0	Hydrophobic	false
CE1	CD2	LEU- 71	4.4	0	Hydrophobic	false
CE1	CG2	THR- 76	4.15	0	Hydrophobic	false
N	OD1	ASP- 81	3.03	157.99	H-Bond (Ligand Donor)	false
N	OD1	ASP- 81	3.03	0	Ionic (Ligand Cationic)	false
N	OH	TYR- 175	2.67	165.49	H-Bond (Ligand Donor)	false
N	OE1	GLN- 179	2.93	159.18	H-Bond (Ligand Donor)	false
CE2	CG	GLN- 179	3.44	0	Hydrophobic	false
CZ	CG	GLN- 179	3.64	0	Hydrophobic	false
CZ	CB	ASP- 182	4.14	0	Hydrophobic	false
OH	OD1	ASP- 182	2.96	150.12	H-Bond (Ligand Donor)	false
O2'	N	GLY- 198	3.01	128.23	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 200	2.9	136.85	H-Bond (Ligand Donor)	false
C3'	CG	GLN- 201	4.17	0	Hydrophobic	false
N1	N	ILE- 228	2.89	131.43	H-Bond (Protein Donor)	false
N6	O	ILE- 228	3.25	158.24	H-Bond (Ligand Donor)	false