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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:

2jj1

2.700 Å

X-ray

2007-07-03

Molecular Function:
Binding Site :

Uniprot Annotation

Name:ATP synthase subunit alpha, mitochondrialATP synthase subunit beta, mitochondrialATP synthase subunit gamma, mitochondrial
ID:ATPA_BOVINATPB_BOVINATPG_BOVIN
AC:P19483P00829P05631
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/3.6.3.14/


Chains:

Chain Name:Percentage of Residues
within binding site
B17 %
C20 %
E7 %
F20 %
G37 %


Ligand binding site composition:

B-Factor:21.864
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.167486.000

% Hydrophobic% Polar
59.7240.28
According to VolSite

Ligand :
2jj1_1 Structure
HET Code: PIT
Formula: C14H12O4
Molecular weight: 244.243 g/mol
DrugBank ID: DB08399
Buried Surface Area:63.1 %
Polar Surface area: 80.92 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-5.9356124.95128.8935


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
C3CBALA- 2563.710Hydrophobic
C1CBTHR- 2594.160Hydrophobic
C9CGLYS- 2603.390Hydrophobic
C14CBILE- 2633.710Hydrophobic
C12CGGLU- 2643.840Hydrophobic
C11CBALA- 2784.280Hydrophobic
C10CG2VAL- 2793.710Hydrophobic
C3CGARG- 2913.780Hydrophobic
O3NGLU- 2922.83128.52H-Bond
(Protein Donor)
C2CGGLU- 2924.040Hydrophobic
O2OHOH- 20563.02143.87H-Bond
(Protein Donor)