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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:

3h0l

2.300 Å

X-ray

2009-04-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
ID:GATB_AQUAE
AC:O66766
Organism:Aquifex aeolicus
Reign:Bacteria
TaxID:224324
EC Number:6.3.5


Chains:

Chain Name:Percentage of Residues
within binding site
K100 %


Ligand binding site composition:

B-Factor:51.627
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.089270.000

% Hydrophobic% Polar
48.7551.25
According to VolSite

Ligand :
3h0l_4 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:52.7 %
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
-134.7319.4118511.0153


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
C4'CGGLU- 123.780Hydrophobic
C3'CG1VAL- 1553.490Hydrophobic
O3'OTHR- 1562.87147.6H-Bond
(Ligand Donor)
O2'OTHR- 1562.79145.46H-Bond
(Ligand Donor)
C2'CGPRO- 1584.450Hydrophobic
C1'CBASN- 1973.810Hydrophobic
N6OGSER- 1993.32129.84H-Bond
(Ligand Donor)
N1OGSER- 1992.73169.67H-Bond
(Protein Donor)