scPDB - 1n75 entry

Protein Data Bank Entry:

PDB ID : 1n75

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2002-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate--tRNA ligase
ID:	SYE_THET8
AC:	P27000
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	6.1.1.17

Chains:

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

Ligand binding site composition:

B-Factor:	29.739
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.485	870.750

% Hydrophobic	% Polar
40.70	59.30
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	57.54 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
39.1844	5.63703	46.1424

Binding mode :

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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
O2B	NE2	HIS- 15	2.9	156.35	H-Bond (Protein Donor)	false
C5'	CB	HIS- 15	4.24	0	Hydrophobic	false
O2'	OE2	GLU- 208	2.69	157.06	H-Bond (Ligand Donor)	false
N6	O	LEU- 236	2.97	159.17	H-Bond (Ligand Donor)	false
N1	N	LEU- 236	2.88	166.28	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 243	3.02	146.99	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 243	3.02	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 243	3.92	0	Ionic (Protein Cationic)	false
N6	O	ILE- 244	3.14	156.2	H-Bond (Ligand Donor)	false
O2G	OG	SER- 245	2.51	154.31	H-Bond (Protein Donor)	false
O2B	N	LYS- 246	2.82	155.38	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 246	3.03	173.74	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 246	3.03	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 247	3.43	0	Ionic (Protein Cationic)	false
O3G	NE	ARG- 247	2.58	141.3	H-Bond (Protein Donor)	false
O1G	MG	MG- 502	2.02	0	Metal Acceptor	false
O1B	MG	MG- 502	2.03	0	Metal Acceptor	false
O1A	MG	MG- 502	2.09	0	Metal Acceptor	false