scPDB - 3a7r entry

Protein Data Bank Entry:

PDB ID : 3a7r

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-10-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lipoate-protein ligase A
ID:	LPLA_ECOLI
AC:	P32099
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.3.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	13.255
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.872	708.750

% Hydrophobic	% Polar
52.86	47.14
According to VolSite

Ligand :

HET Code:	LAQ
Formula:	C18H25N5O8PS2
Molecular weight:	534.524 g/mol
DrugBank ID:	-
Buried Surface Area:	80.98 %
Polar Surface area:	255.38 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-16.1341	-37.0214	5.72603

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
S17	CH2	TRP- 37	3.69	0	Hydrophobic	false
C17	CZ2	TRP- 37	3.53	0	Hydrophobic	false
S15	CG1	VAL- 44	3.74	0	Hydrophobic	false
S17	CG1	VAL- 44	3.82	0	Hydrophobic	false
C13	CD	ARG- 70	4.46	0	Hydrophobic	false
S17	CD	ARG- 70	4.05	0	Hydrophobic	false
S15	CD	ARG- 70	3.82	0	Hydrophobic	false
O3P	N	GLY- 75	3.2	129.89	H-Bond (Protein Donor)	false
C13	CG2	VAL- 77	4.12	0	Hydrophobic	false
S15	CG2	VAL- 77	3.68	0	Hydrophobic	false
C5'	CG1	VAL- 77	4.2	0	Hydrophobic	false
C11	CG1	VAL- 77	3.71	0	Hydrophobic	false
N7	N	PHE- 78	3.15	162.39	H-Bond (Protein Donor)	false
N6	O	PHE- 78	2.87	153.4	H-Bond (Ligand Donor)	false
N6	OD1	ASN- 83	3.12	156.97	H-Bond (Ligand Donor)	false
C17	SG	CYS- 85	4.17	0	Hydrophobic	false
O1P	ND2	ASN- 121	3.09	167.01	H-Bond (Protein Donor)	false
O10	NZ	LYS- 133	2.98	154.87	H-Bond (Protein Donor)	false
C1'	CD	LYS- 133	4.32	0	Hydrophobic	false
C13	CB	ALA- 138	4.08	0	Hydrophobic	false
C17	CB	HIS- 149	4.08	0	Hydrophobic	false
C14	CG2	THR- 151	4.16	0	Hydrophobic	false
C16	CG2	THR- 151	4.03	0	Hydrophobic	false
N1	OG1	THR- 151	2.76	149.44	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 165	4.17	0	Hydrophobic	false
O2P	N	VAL- 180	2.75	167.45	H-Bond (Protein Donor)	false
O2'	N	SER- 182	3.06	169.97	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 184	3.67	0	Hydrophobic	false