scPDB - 1b7y entry

Protein Data Bank Entry:

PDB ID : 1b7y

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1999-01-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylalanine--tRNA ligase alpha subunit
ID:	SYFA_THETH
AC:	P27001
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	6.1.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	58.741
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.472	853.875

% Hydrophobic	% Polar
44.66	55.34
According to VolSite

Ligand :

HET Code:	FYA
Formula:	C19H25N6O7P
Molecular weight:	480.412 g/mol
DrugBank ID:	-
Buried Surface Area:	74.67 %
Polar Surface area:	215.35 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.9958	62.3106	16.9433

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
C	CZ2	TRP- 149	3.99	0	Hydrophobic	false
N	OG	SER- 180	3.29	164.38	H-Bond (Ligand Donor)	false
O1P	CZ	ARG- 204	3.52	0	Ionic (Protein Cationic)	false
O1P	NH1	ARG- 204	3.12	133.09	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 204	3.14	132.63	H-Bond (Protein Donor)	false
N6	OE2	GLU- 206	2.79	150.5	H-Bond (Ligand Donor)	false
N6	O	GLU- 213	2.89	137.59	H-Bond (Ligand Donor)	false
N1	N	GLU- 213	3.12	168.56	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 216	4.25	0	Hydrophobic	false
O4'	NE2	GLN- 218	3.48	142.37	H-Bond (Protein Donor)	false
C5'	CG	GLN- 218	4.08	0	Hydrophobic	false
N	OE1	GLU- 220	3.46	128.72	H-Bond (Ligand Donor)	false
N	OE1	GLU- 220	3.46	0	Ionic (Ligand Cationic)	false
N	OE2	GLU- 220	3.99	0	Ionic (Ligand Cationic)	false
C	CE1	PHE- 258	3.93	0	Hydrophobic	false
CB	CE1	PHE- 258	4.19	0	Hydrophobic	false
CD1	CZ	PHE- 258	3.46	0	Hydrophobic	false
CE1	CG2	VAL- 261	4.12	0	Hydrophobic	false
CZ	CG1	VAL- 261	3.89	0	Hydrophobic	false
O3'	O	LEU- 280	3.22	149.62	H-Bond (Ligand Donor)	false
CE2	CB	ALA- 314	4.13	0	Hydrophobic	false
C1'	CG	ARG- 321	4.32	0	Hydrophobic	false