scPDB - 1c0a entry

Protein Data Bank Entry:

PDB ID : 1c0a

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1999-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate--tRNA ligase
ID:	SYD_ECOLI
AC:	P21889
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.925
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.203	813.375

% Hydrophobic	% Polar
39.83	60.17
According to VolSite

Ligand :

HET Code:	AMO
Formula:	C14H18N6O10P
Molecular weight:	461.301 g/mol
DrugBank ID:	DB01895
Buried Surface Area:	74.55 %
Polar Surface area:	272.54 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
54.2467	39.2774	-10.939

Binding mode :

What is Poseview ?

2D View
3D View

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
N	OE1	GLN- 195	2.65	164.11	H-Bond (Ligand Donor)	false
OD1	NZ	LYS- 198	2.64	163.83	H-Bond (Protein Donor)	false
OD1	NZ	LYS- 198	2.64	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 217	3.64	0	Ionic (Protein Cationic)	false
O1P	NH1	ARG- 217	2.85	174.04	H-Bond (Protein Donor)	false
O	NH2	ARG- 217	2.72	130.28	H-Bond (Protein Donor)	false
N1	N	GLN- 226	3.15	165.94	H-Bond (Protein Donor)	false
N6	O	GLN- 226	2.96	133.44	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 229	3.85	0	Hydrophobic	false
DuAr	DuAr	PHE- 229	3.44	0	Aromatic Face/Face	false
C5'	CG	GLN- 231	4.35	0	Hydrophobic	false
O	NE2	GLN- 231	2.86	172.39	H-Bond (Protein Donor)	false
OD2	NE2	HIS- 448	2.75	163.87	H-Bond (Protein Donor)	false
OD2	NE2	HIS- 449	3.12	146.42	H-Bond (Protein Donor)	false
C3'	CG	GLU- 482	4.48	0	Hydrophobic	false
O3'	OE2	GLU- 482	2.57	164.41	H-Bond (Ligand Donor)	false
O2'	O	GLU- 482	2.76	172.87	H-Bond (Ligand Donor)	false
OD1	CZ	ARG- 489	3.52	0	Ionic (Protein Cationic)	false
OD2	CZ	ARG- 489	3.43	0	Ionic (Protein Cationic)	false
OD2	NH1	ARG- 489	2.72	153.79	H-Bond (Protein Donor)	false
OD2	NH2	ARG- 489	3.21	132.28	H-Bond (Protein Donor)	false
C5'	CB	ALA- 532	3.95	0	Hydrophobic	false
CB	CB	ALA- 532	3.52	0	Hydrophobic	false
C2'	CD	ARG- 537	4.13	0	Hydrophobic	false
N3	O	HOH- 1003	2.68	154.24	H-Bond (Protein Donor)	false
N	O	HOH- 1133	2.86	168.91	H-Bond (Ligand Donor)	false