scPDB - 1wnz entry

Protein Data Bank Entry:

PDB ID : 1wnz

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2004-08-11

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:	35.370
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.535	364.500

% Hydrophobic	% Polar
38.89	61.11
According to VolSite

Ligand :

HET Code:	2VA
Formula:	C15H24N7O4
Molecular weight:	366.396 g/mol
DrugBank ID:	-
Buried Surface Area:	61.17 %
Polar Surface area:	176.05 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
66.9521	31.2836	19.4968

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
N7	O	HOH- 12	2.77	179.96	H-Bond (Protein Donor)	false
C3'	CZ3	TRP- 227	4.31	0	Hydrophobic	false
C5'	CZ3	TRP- 227	3.92	0	Hydrophobic	false
C3'	CB	THR- 228	4.41	0	Hydrophobic	false
O3'	OG1	THR- 228	2.94	163.47	H-Bond (Protein Donor)	false
O3'	N	THR- 229	3.16	160.74	H-Bond (Protein Donor)	false
C5'	CG2	THR- 229	3.78	0	Hydrophobic	false
CG2	CG2	THR- 233	4.01	0	Hydrophobic	false
CG1	CB	THR- 233	4.41	0	Hydrophobic	false
N1	N	SER- 310	2.87	162.26	H-Bond (Protein Donor)	false
N6	O	SER- 310	2.73	159.65	H-Bond (Ligand Donor)	false
N6	O	ASP- 313	2.86	130.23	H-Bond (Ligand Donor)	false
C1'	CG1	VAL- 318	4.25	0	Hydrophobic	false
N	O	HIS- 319	2.96	175.75	H-Bond (Ligand Donor)	false
CG1	CB	ALA- 321	3.95	0	Hydrophobic	false
CG1	CB	PHE- 324	3.57	0	Hydrophobic	false
N	OD2	ASP- 328	2.7	132.92	H-Bond (Ligand Donor)	false
N	OD1	ASP- 328	3.47	123.11	H-Bond (Ligand Donor)	false
N	OD2	ASP- 328	2.7	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 328	3.47	0	Ionic (Ligand Cationic)	false