Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4nau

2.330 Å

X-ray

2013-10-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphopantetheine adenylyltransferase
ID:COAD_STAAW
AC:P63820
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:196620
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A3 %
B97 %


Ligand binding site composition:

B-Factor:42.171
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.013594.000

% Hydrophobic% Polar
32.3967.61
According to VolSite

Ligand :
4nau_2 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:61.82 %
Polar Surface area: 329.24 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-15.9659-26.287341.6637


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2ANSER- 113.2127.98H-Bond
(Protein Donor)
O2ANPHE- 122.89165.92H-Bond
(Protein Donor)
O2ANE2HIS- 193.35123.32H-Bond
(Protein Donor)
O3'NGLY- 903.21163.57H-Bond
(Protein Donor)
O2'OGLY- 902.87154.52H-Bond
(Ligand Donor)
O2BCZARG- 923.260Ionic
(Protein Cationic)
N1OGSER- 1213.22156.89H-Bond
(Protein Donor)
N6OTYR- 1252.89151.26H-Bond
(Ligand Donor)
N6OILE- 1283.16127.5H-Bond
(Ligand Donor)
O3GOGSER- 1293.34128.85H-Bond
(Protein Donor)
O3GNSER- 1312.7159.13H-Bond
(Protein Donor)
O3'OHOH- 3203.3161.86H-Bond
(Ligand Donor)