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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3gie

2.650 Å

X-ray

2009-03-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Sensor histidine kinase DesK
ID:DESK_BACSU
AC:O34757
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:2.7.13.3


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:99.999
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.039550.125

% Hydrophobic% Polar
66.8733.13
According to VolSite

Ligand :
3gie_2 Structure
HET Code: ACP
Formula: C11H14N5O12P3
Molecular weight: 501.176 g/mol
DrugBank ID: DB03909
Buried Surface Area:60.6 %
Polar Surface area: 310.64 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
31.089522.079128.3584


Binding mode :
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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
O3GMG MG- 12.050Metal Acceptor
O2BMG MG- 12.050Metal Acceptor
O1AMG MG- 12.060Metal Acceptor
O1BNE2HIS- 2973.4149.62H-Bond
(Protein Donor)
C1'CE1PHE- 3243.580Hydrophobic
N3NLYS- 3252.62165.25H-Bond
(Protein Donor)
C2'CBLYS- 3254.070Hydrophobic
C4'CBSER- 3303.380Hydrophobic
O1GOGSER- 3323.41161.77H-Bond
(Protein Donor)
O1GNGLY- 3362.71152.94H-Bond
(Protein Donor)
O1ANLEU- 3373.34126.59H-Bond
(Protein Donor)
O2ANLEU- 3373.29151.68H-Bond
(Protein Donor)