Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2ag0

2.580 Å

X-ray

2005-07-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Benzaldehyde lyase
ID:Q9F4L3_PSEFL
AC:Q9F4L3
Organism:Pseudomonas fluorescens
Reign:Bacteria
TaxID:294
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A71 %
B29 %


Ligand binding site composition:

B-Factor:44.615
Number of residues:42
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.656330.750

% Hydrophobic% Polar
51.0248.98
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2ag0HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
2ag0_1 Structure
HET Code: TPP
Formula: C12H16N4O7P2S
Molecular weight: 422.291 g/mol
DrugBank ID: -
Buried Surface Area:79.98 %
Polar Surface area: 225.32 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
41.6127-26.74986.74812
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2ag0RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
N1'OE2GLU- 502.86152.46H-Bond
(Ligand Donor)
C5'CG2THR- 733.990Hydrophobic
S1CBALA- 3943.70Hydrophobic
C7CBALA- 3943.840Hydrophobic
O2BNLEU- 3953.21149.97H-Bond
(Protein Donor)
O1BOG1THR- 3963.03160.05H-Bond
(Protein Donor)
O1BNTHR- 3963.41137.68H-Bond
(Protein Donor)
N4'OGLY- 4192.93168.28H-Bond
(Ligand Donor)
CM2CBSER- 4204.070Hydrophobic
N3'NMET- 4213.33159.12H-Bond
(Protein Donor)
C5'CGMET- 4214.230Hydrophobic
C7SDMET- 4214.190Hydrophobic
S1CEMET- 4213.830Hydrophobic
O1ANGLY- 4492.73149.94H-Bond
(Protein Donor)
O2ANSER- 4502.83141.76H-Bond
(Protein Donor)
O2AOGSER- 4502.67163.66H-Bond
(Protein Donor)
CM2CZTYR- 4534.10Hydrophobic
O3BND2ASN- 4753.33137.85H-Bond
(Protein Donor)
C7CE3TRP- 4784.150Hydrophobic
O3BNGLY- 4792.83139.9H-Bond
(Protein Donor)
S1CBALA- 4804.130Hydrophobic
O2BNALA- 4803.22150.67H-Bond
(Protein Donor)
C7'CG2THR- 4814.180Hydrophobic
C2CG2THR- 4813.610Hydrophobic
O1AMG MG- 6012.210Metal Acceptor
O3BMG MG- 6012.010Metal Acceptor
O1BOHOH- 50112.7120.26H-Bond
(Protein Donor)