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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:

5a03

1.850 Å

X-ray

2015-04-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glucose-fructose oxidoreductase
ID:Q9A8X3_CAUCR
AC:Q9A8X3
Organism:Caulobacter crescentus
Reign:Bacteria
TaxID:190650
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:22.874
Number of residues:45
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 2
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.260830.250

% Hydrophobic% Polar
39.8460.16
According to VolSite

Ligand :
5a03_4 Structure
HET Code: NDP
Formula: C21H26N7O17P3
Molecular weight: 741.389 g/mol
DrugBank ID: DB02338
Buried Surface Area:66.66 %
Polar Surface area: 404.9 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 5
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
31.9317-31.858911.7607


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
O3XNLEU- 142.98154.22H-Bond
(Protein Donor)
O2ANTYR- 162.73167.59H-Bond
(Protein Donor)
O1NNTYR- 173.11170.91H-Bond
(Protein Donor)
DuArDuArTYR- 173.860Aromatic Face/Face
C5NCBTYR- 173.660Hydrophobic
O1XNGLY- 402.91155.44H-Bond
(Protein Donor)
O2XOG1THR- 412.79148.5H-Bond
(Protein Donor)
O2XNZLYS- 442.76176.09H-Bond
(Protein Donor)
O2XNZLYS- 442.760Ionic
(Protein Cationic)
O3XNZLYS- 443.950Ionic
(Protein Cationic)
C4DCG2ILE- 803.860Hydrophobic
C1BCG2THR- 814.490Hydrophobic
O3DOD1ASN- 832.9162.15H-Bond
(Ligand Donor)
O3DNE2HIS- 862.85125.31H-Bond
(Protein Donor)
C4DCBGLU- 1034.290Hydrophobic
N7NOE1GLU- 1032.83169.27H-Bond
(Ligand Donor)
O2DOLYS- 1042.75157.74H-Bond
(Ligand Donor)
O2DNZLYS- 1043.19167.64H-Bond
(Protein Donor)
C3NCDLYS- 1044.350Hydrophobic
O7NNEARG- 1322.76148.74H-Bond
(Protein Donor)
O7NNH2ARG- 1322.89139.28H-Bond
(Protein Donor)
O1ANE1TRP- 1712.93132.75H-Bond
(Protein Donor)
O3NE1TRP- 1713.01156.92H-Bond
(Protein Donor)
C5DCZ2TRP- 1713.910Hydrophobic
C3DCH2TRP- 1713.590Hydrophobic
O2NNH2ARG- 1722.76162.28H-Bond
(Protein Donor)
O2NNH1ARG- 1723.23133.82H-Bond
(Protein Donor)
O5DNH2ARG- 1723.37123.8H-Bond
(Protein Donor)
O2NCZARG- 1723.430Ionic
(Protein Cationic)
O1NOHOH- 20012.7168.45H-Bond
(Protein Donor)
O2DOHOH- 20812.75179.95H-Bond
(Protein Donor)