scPDB - 3ag6 entry

Protein Data Bank Entry:

PDB ID : 3ag6

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-03-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate synthetase
ID:	PANC_STAA8
AC:	Q2FV22
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93061
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.716
Number of residues:	49
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.407	536.625

% Hydrophobic	% Polar
37.11	62.89
According to VolSite

Ligand :

HET Code:	PAJ
Formula:	C16H23N5O10P
Molecular weight:	476.355 g/mol
DrugBank ID:	DB02694
Buried Surface Area:	76.64 %
Polar Surface area:	245.23 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-4.35875	-2.23425	-43.329

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
C14	CB	PRO- 29	4.03	0	Hydrophobic	false
C15	CG	PRO- 29	4.24	0	Hydrophobic	false
C5'	CB	THR- 30	4.08	0	Hydrophobic	false
O2P	N	MET- 31	2.92	162.48	H-Bond (Protein Donor)	false
C12	CG	MET- 31	4.02	0	Hydrophobic	false
C14	CG	MET- 31	4.03	0	Hydrophobic	false
O2P	NE2	HIS- 38	3.35	136.65	H-Bond (Protein Donor)	false
C4'	CE	MET- 41	3.63	0	Hydrophobic	false
C1'	CE	MET- 41	3.66	0	Hydrophobic	false
O13	NE2	GLN- 62	2.93	165.92	H-Bond (Protein Donor)	false
O14	OE1	GLN- 62	2.61	171.98	H-Bond (Ligand Donor)	false
C16	CG1	VAL- 132	3.64	0	Hydrophobic	false
C15	CG2	VAL- 133	4.16	0	Hydrophobic	false
C16	CG2	VAL- 133	4.08	0	Hydrophobic	false
C15	CE2	PHE- 147	3.87	0	Hydrophobic	false
O3'	N	GLY- 148	3.1	161.11	H-Bond (Protein Donor)	false
O2'	N	GLY- 148	3.07	124.18	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 151	2.81	145.33	H-Bond (Ligand Donor)	false
O11	NE2	GLN- 154	3.24	152.71	H-Bond (Protein Donor)	false
O13	OE1	GLN- 154	2.59	133.4	H-Bond (Ligand Donor)	false
N6	O	VAL- 177	2.85	161.03	H-Bond (Ligand Donor)	false
N1	N	VAL- 177	2.79	176.75	H-Bond (Protein Donor)	false
N6	O	LYS- 185	2.7	174.08	H-Bond (Ligand Donor)	false
O3'	O	HOH- 431	2.71	179.34	H-Bond (Ligand Donor)	false
N7	O	HOH- 442	3.04	138.42	H-Bond (Protein Donor)	false