Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4lnk

2.870 Å

X-ray

2013-07-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutamine synthetase
ID:GLNA_BACSU
AC:P12425
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:6.3.1.2


Chains:

Chain Name:Percentage of Residues
within binding site
A17 %
F83 %


Ligand binding site composition:

B-Factor:70.976
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.127840.375

% Hydrophobic% Polar
31.7368.27
According to VolSite

Ligand :
4lnk_6 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:54.78 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
46.139754.202918.3717


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
O2BNZLYS- 443.850Ionic
(Protein Cationic)
O1ANZLYS- 442.870Ionic
(Protein Cationic)
O2ANZLYS- 443.850Ionic
(Protein Cationic)
O2'OPHE- 1993.08173.32H-Bond
(Ligand Donor)
C1'CBASN- 2473.930Hydrophobic
N1OGSER- 2492.65169.15H-Bond
(Protein Donor)
O3BOGSER- 3253.25154.59H-Bond
(Protein Donor)
O1BOGSER- 3292.62120.11H-Bond
(Protein Donor)
C1'CDARG- 33140Hydrophobic