scPDB - 1pfy entry

Protein Data Bank Entry:

PDB ID : 1pfy

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2003-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine--tRNA ligase
ID:	SYM_ECOLI
AC:	P00959
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	10.756
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.745	570.375

% Hydrophobic	% Polar
50.30	49.70
According to VolSite

Ligand :

HET Code:	MSP
Formula:	C15H27N7O7S2
Molecular weight:	481.548 g/mol
DrugBank ID:	DB02229
Buried Surface Area:	73.04 %
Polar Surface area:	254.78 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	3
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.0233	11.8871	25.0113

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
CB	CB	ALA- 12	4.11	0	Hydrophobic	false
SD	CB	ALA- 12	3.92	0	Hydrophobic	false
C4'	CB	ALA- 12	3.92	0	Hydrophobic	false
N2	O	LEU- 13	2.65	172.5	H-Bond (Ligand Donor)	false
CE	CG	LEU- 13	4	0	Hydrophobic	false
CG	CB	LEU- 13	4.24	0	Hydrophobic	false
O1S	N	TYR- 15	3.15	161.72	H-Bond (Protein Donor)	false
O1S	NE2	HIS- 24	3.42	128.52	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 27	2.73	164.52	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 52	2.8	154.73	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 52	2.8	0	Ionic (Ligand Cationic)	false
CG	CH2	TRP- 253	3.54	0	Hydrophobic	false
SD	CZ3	TRP- 253	4.08	0	Hydrophobic	false
CG	CB	ALA- 256	4.39	0	Hydrophobic	false
CE	CB	ALA- 256	3.81	0	Hydrophobic	false
CE	CB	PRO- 257	4.3	0	Hydrophobic	false
CE	CZ	TYR- 260	3.7	0	Hydrophobic	false
O3'	N	GLY- 294	3.03	145.45	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 296	2.57	156.35	H-Bond (Ligand Donor)	false
CB	CD1	ILE- 297	4.1	0	Hydrophobic	false
SD	CD1	ILE- 297	4.48	0	Hydrophobic	false
C3'	CD1	ILE- 297	3.8	0	Hydrophobic	false
N1	N	VAL- 326	2.86	164.86	H-Bond (Protein Donor)	false