Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3zcn

1.700 Å

X-ray

2012-11-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Adenosine monophosphate-protein transferase SoFic
ID:SOFIC_SHEON
AC:Q8E9K5
Organism:Shewanella oneidensis
Reign:Bacteria
TaxID:211586
EC Number:2.7.7.n1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:15.729
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.222904.500

% Hydrophobic% Polar
45.5254.48
According to VolSite

Ligand :
3zcn_2 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:65.73 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
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
-3.474069.77106-30.8395


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
C5'CGGLU- 734.330Hydrophobic
O3'OE2GLU- 732.67157.13H-Bond
(Ligand Donor)
C1'CD2LEU- 1454.490Hydrophobic
C1'CGGLU- 1954.140Hydrophobic
O1ANE2HIS- 1982.87166.89H-Bond
(Protein Donor)
O5'NE2HIS- 1983.24123.22H-Bond
(Protein Donor)
O3GNGLY- 2032.55125.2H-Bond
(Protein Donor)
O3BNGLY- 2033.02158.92H-Bond
(Protein Donor)
O2BND2ASN- 2042.84165.99H-Bond
(Protein Donor)
O2BNASN- 2043.16151.39H-Bond
(Protein Donor)
O1BNGLY- 2052.95170.15H-Bond
(Protein Donor)
O3GNH2ARG- 2062.59141.06H-Bond
(Protein Donor)
O3GCZARG- 2063.760Ionic
(Protein Cationic)
O3'NH1ARG- 2092.94163.67H-Bond
(Protein Donor)
O2'OHTYR- 2402.93159.66H-Bond
(Ligand Donor)
C2'CE2TYR- 2403.680Hydrophobic
C3'CE1TYR- 2414.050Hydrophobic
C2'CD1LEU- 2443.890Hydrophobic
O1BOHOH- 21502.58154.93H-Bond
(Protein Donor)