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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:

3ed1

1.900 Å

X-ray

2008-09-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gibberellin receptor GID1
ID:GID1_ORYSJ
AC:Q6L545
Organism:Oryza sativa subsp. japonica
Reign:Eukaryota
TaxID:39947
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
F100 %


Ligand binding site composition:

B-Factor:23.550
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.732438.750

% Hydrophobic% Polar
49.2350.77
According to VolSite

Ligand :
3ed1_6 Structure
HET Code: GA3
Formula: C19H21O6
Molecular weight: 345.366 g/mol
DrugBank ID: DB07814
Buried Surface Area:78.15 %
Polar Surface area: 106.89 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 5
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
35.955944.27156.0726


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
C11CG2ILE- 243.720Hydrophobic
C12CBLYS- 284.150Hydrophobic
C15CD2TYR- 314.20Hydrophobic
C9CE2TYR- 314.450Hydrophobic
O71NGLY- 1223.12122.03H-Bond
(Protein Donor)
O71OGSER- 1232.71167.64H-Bond
(Protein Donor)
C3CD1ILE- 1333.80Hydrophobic
C3CZTYR- 1344.480Hydrophobic
O31OHTYR- 1342.58141.88H-Bond
(Ligand Donor)
O71OGSER- 1983.11125.2H-Bond
(Protein Donor)
O72OGSER- 1982.81175.33H-Bond
(Protein Donor)
C18CBSER- 1983.950Hydrophobic
C12CBPHE- 2454.490Hydrophobic
C14CG2VAL- 2463.920Hydrophobic
O13OD2ASP- 2503.08156.87H-Bond
(Ligand Donor)
C3CD1LEU- 3304.070Hydrophobic