scPDB - 1ivs entry

Protein Data Bank Entry:

PDB ID : 1ivs

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2002-03-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Valine--tRNA ligase
ID:	SYV_THETH
AC:	P96142
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	6.1.1.9

Chains:

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

Ligand binding site composition:

B-Factor:	36.049
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.310	435.375

% Hydrophobic	% Polar
41.86	58.14
According to VolSite

Ligand :

HET Code:	VAA
Formula:	C15H25N8O6S
Molecular weight:	445.474 g/mol
DrugBank ID:	-
Buried Surface Area:	78.12 %
Polar Surface area:	230.59 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
174.744	120.02	18.5097

Binding mode :

What is Poseview ?

2D View
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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
CG1	CB	PRO- 41	3.53	0	Hydrophobic	false
C4'	CB	PRO- 41	3.99	0	Hydrophobic	false
N	O	PRO- 42	2.82	152.2	H-Bond (Ligand Donor)	false
CG1	CG	PRO- 42	4.15	0	Hydrophobic	false
CG2	CG	PRO- 42	4.41	0	Hydrophobic	false
N	OD1	ASN- 44	2.6	168.73	H-Bond (Ligand Donor)	false
O1S	N	ASN- 44	3.48	156.77	H-Bond (Protein Donor)	false
O1S	NE2	HIS- 53	3.08	142.03	H-Bond (Protein Donor)	false
N	OD2	ASP- 81	3.25	153.43	H-Bond (Ligand Donor)	false
N	OD2	ASP- 81	3.25	0	Ionic (Ligand Cationic)	false
CG2	CZ3	TRP- 456	3.71	0	Hydrophobic	false
CG2	CB	SER- 459	3.55	0	Hydrophobic	false
C3'	CB	THR- 487	4.43	0	Hydrophobic	false
O3'	OG1	THR- 487	2.73	164.51	H-Bond (Protein Donor)	false
O2'	N	GLY- 488	2.74	133.14	H-Bond (Protein Donor)	false
O3'	N	GLY- 488	3.49	154.16	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 490	2.7	173.03	H-Bond (Ligand Donor)	false
CB	CD1	ILE- 491	3.77	0	Hydrophobic	false
C3'	CD1	ILE- 491	3.63	0	Hydrophobic	false
CG2	CE2	TRP- 495	3.64	0	Hydrophobic	false
CB	CD2	TRP- 495	4.18	0	Hydrophobic	false
N3	NE2	HIS- 518	3.38	151.77	H-Bond (Protein Donor)	false
N1	N	VAL- 521	2.96	157.17	H-Bond (Protein Donor)	false
N6	O	VAL- 521	3.25	169.58	H-Bond (Ligand Donor)	false
N6	O	MET- 529	2.8	152.79	H-Bond (Ligand Donor)	false