scPDB - 1i6k entry

Protein Data Bank Entry:

PDB ID : 1i6k

Resolution :1.720 Å

Experimental Method : X-ray

Deposition Date : 2001-03-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan--tRNA ligase
ID:	SYW_GEOSE
AC:	P00953
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	6.1.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	21.785
Number of residues:	53
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.434	614.250

% Hydrophobic	% Polar
32.42	67.58
According to VolSite

Ligand :

HET Code:	TYM
Formula:	C21H24N7O8P
Molecular weight:	533.431 g/mol
DrugBank ID:	DB01831
Buried Surface Area:	82.18 %
Polar Surface area:	248.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
53.0962	22.9433	41.1719

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
CZ2	CE2	PHE- 5	3.44	0	Hydrophobic	false
CZ3	CB	SER- 6	4.28	0	Hydrophobic	false
C5'	CG1	ILE- 8	3.66	0	Hydrophobic	false
O1P	N	GLN- 9	2.81	167.53	H-Bond (Protein Donor)	false
O	NE2	GLN- 9	3.2	134.26	H-Bond (Protein Donor)	false
O4'	ND2	ASN- 18	3.14	168.01	H-Bond (Protein Donor)	false
C1'	CB	ALA- 22	4.21	0	Hydrophobic	false
C4'	CB	ALA- 22	3.62	0	Hydrophobic	false
CB	CG2	VAL- 40	3.82	0	Hydrophobic	false
CA	SD	MET- 129	4.41	0	Hydrophobic	false
CE2	CG	MET- 129	3.77	0	Hydrophobic	false
CZ3	CE	MET- 129	3.78	0	Hydrophobic	false
NE1	OD1	ASP- 132	2.79	169.87	H-Bond (Ligand Donor)	false
CZ2	CB	ASP- 132	4.1	0	Hydrophobic	false
CZ2	CG1	ILE- 133	3.71	0	Hydrophobic	false
CH2	CG1	VAL- 141	3.57	0	Hydrophobic	false
C3'	CB	VAL- 143	4.44	0	Hydrophobic	false
CZ3	CG1	VAL- 143	3.66	0	Hydrophobic	false
O2'	N	GLY- 144	2.87	132.93	H-Bond (Protein Donor)	false
O3'	N	GLY- 144	3.22	151.02	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 146	2.65	168.38	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 146	3.24	128.86	H-Bond (Ligand Donor)	false
CA	CG	GLN- 147	4.11	0	Hydrophobic	false
C3'	CG	GLN- 147	4.17	0	Hydrophobic	false
N1	N	ILE- 183	2.92	156.31	H-Bond (Protein Donor)	false
N6	O	ILE- 183	2.88	161.44	H-Bond (Ligand Donor)	false
N7	NZ	LYS- 192	2.83	122.59	H-Bond (Protein Donor)	false
N6	O	MET- 193	3.12	152.94	H-Bond (Ligand Donor)	false
NH3	O	HOH- 494	3.44	165.36	H-Bond (Ligand Donor)	false
O2P	O	HOH- 753	2.66	151.9	H-Bond (Protein Donor)	false