scPDB - 1jzs entry

Protein Data Bank Entry:

PDB ID : 1jzs

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-09-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isoleucine--tRNA ligase
ID:	SYI_THET8
AC:	P56690
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	6.1.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	39.132
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.051	1015.875

% Hydrophobic	% Polar
37.54	62.46
According to VolSite

Ligand :

HET Code:	MRC
Formula:	C26H43O9
Molecular weight:	499.614 g/mol
DrugBank ID:	DB00410
Buried Surface Area:	50.36 %
Polar Surface area:	148.88 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
-26.7828	8.88289	-29.4001

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
C14	CG	PRO- 46	3.85	0	Hydrophobic	false
C5'	CB	HIS- 54	4.1	0	Hydrophobic	false
C8'	CG2	VAL- 55	4.27	0	Hydrophobic	false
C13	CZ3	TRP- 518	4.21	0	Hydrophobic	false
C14	CB	SER- 521	3.85	0	Hydrophobic	false
C7	CB	GLU- 550	4.13	0	Hydrophobic	false
C17	CG	GLU- 550	4.03	0	Hydrophobic	false
O7	OE1	GLU- 550	3.02	164.48	H-Bond (Ligand Donor)	false
O7	N	GLY- 551	2.98	133.59	H-Bond (Protein Donor)	false
O6	N	GLY- 551	2.96	123.15	H-Bond (Protein Donor)	false
O6	OD2	ASP- 553	2.74	145.64	H-Bond (Ligand Donor)	false
C7	CG	GLN- 554	4.46	0	Hydrophobic	false
C17	CG	GLN- 554	4.46	0	Hydrophobic	false
O6	NE2	GLN- 554	3.49	158.44	H-Bond (Protein Donor)	false
C17	CB	TRP- 558	4.1	0	Hydrophobic	false
C14	CB	TRP- 558	4.1	0	Hydrophobic	false
C15	CG	LEU- 583	4.12	0	Hydrophobic	false
C9'	CB	ILE- 584	4.45	0	Hydrophobic	false
O1B	N	ILE- 584	2.98	177.1	H-Bond (Protein Donor)	false
C7'	CB	MET- 592	4.12	0	Hydrophobic	false