scPDB - 1fyf entry

Protein Data Bank Entry:

PDB ID : 1fyf

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2000-09-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Threonine--tRNA ligase
ID:	SYT_ECOLI
AC:	P0A8M3
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	17.537
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.107	634.500

% Hydrophobic	% Polar
30.85	69.15
According to VolSite

Ligand :

HET Code:	SSA
Formula:	C13H19N7O8S
Molecular weight:	433.397 g/mol
DrugBank ID:	DB03869
Buried Surface Area:	78.99 %
Polar Surface area:	250.09 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
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
27.6171	17.7948	17.6862

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
O9	NH2	ARG- 363	2.87	132.33	H-Bond (Protein Donor)	false
O1S	NH1	ARG- 363	2.99	148.74	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 363	3.12	142.11	H-Bond (Protein Donor)	false
N6	OE2	GLU- 365	2.89	145.38	H-Bond (Ligand Donor)	false
N6	O	VAL- 376	2.83	130.47	H-Bond (Ligand Donor)	false
N1	N	VAL- 376	3.13	170.35	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 379	4.28	0	Hydrophobic	false
O9	NE2	GLN- 381	3.21	165.18	H-Bond (Protein Donor)	false
O4'	NE2	GLN- 381	3.2	146.39	H-Bond (Protein Donor)	false
OG	OD2	ASP- 383	3.44	129.25	H-Bond (Ligand Donor)	false
OG	OD1	ASP- 383	2.53	165.75	H-Bond (Ligand Donor)	false
N10	OH	TYR- 462	3.35	123.06	H-Bond (Ligand Donor)	false
O2S	NE2	GLN- 479	2.93	123.6	H-Bond (Protein Donor)	false
O3'	NE2	GLN- 479	2.79	153.85	H-Bond (Protein Donor)	false
C3'	CG	GLN- 479	4.44	0	Hydrophobic	false
O2'	O	GLN- 479	2.81	166.99	H-Bond (Ligand Donor)	false
O3'	O	CYS- 480	2.72	129.5	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 482	4.08	0	Hydrophobic	false
N8	OE1	GLN- 484	3.07	165.16	H-Bond (Ligand Donor)	false
CB	CB	HIS- 511	4.12	0	Hydrophobic	false
C5'	CB	ALA- 513	4.35	0	Hydrophobic	false
C1'	CB	SER- 517	3.86	0	Hydrophobic	false
N3	OG	SER- 517	2.83	163.71	H-Bond (Protein Donor)	false
C2'	CD	ARG- 520	4.49	0	Hydrophobic	false
OG	ZN	ZN- 650	2.43	0	Metal Acceptor	false
N10	O	HOH- 1012	2.91	154.75	H-Bond (Ligand Donor)	false
N7	O	HOH- 1071	3.01	153.52	H-Bond (Protein Donor)	false