scPDB - 2dxi entry

Protein Data Bank Entry:

PDB ID : 2dxi

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-08-28

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
B	100 %

Ligand binding site composition:

B-Factor:	39.540
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.601	776.250

% Hydrophobic	% Polar
37.83	62.17
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	54.65 %
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
94.6256	77.446	117.589

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
C4'	CD1	ILE- 6	4.07	0	Hydrophobic	false
O3G	OG	SER- 9	3.19	149.33	H-Bond (Protein Donor)	false
O1A	N	SER- 9	2.88	141.89	H-Bond (Protein Donor)	false
O2A	N	SER- 9	3.37	152.33	H-Bond (Protein Donor)	false
O3G	OG1	THR- 11	3.26	144.87	H-Bond (Protein Donor)	false
C5'	CB	THR- 18	3.77	0	Hydrophobic	false
C4'	CB	ILE- 21	4.24	0	Hydrophobic	false
C1'	CG1	ILE- 21	3.41	0	Hydrophobic	false
O2G	NH1	ARG- 47	3.44	151.39	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 47	2.91	152.66	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 47	3.71	0	Ionic (Protein Cationic)	false
O2'	N	ALA- 206	3.14	149.06	H-Bond (Protein Donor)	false
C1'	CB	ALA- 206	3.72	0	Hydrophobic	false
O2'	NE1	TRP- 209	2.7	130.19	H-Bond (Protein Donor)	false
N1	N	LEU- 236	3.47	144.66	H-Bond (Protein Donor)	false