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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:

1s3s

2.900 Å

X-ray

2004-01-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transitional endoplasmic reticulum ATPase
ID:TERA_MOUSE
AC:Q01853
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:3.6.4.6


Chains:

Chain Name:Percentage of Residues
within binding site
A91 %
E9 %


Ligand binding site composition:

B-Factor:44.713
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.203486.000

% Hydrophobic% Polar
45.8354.17
According to VolSite

Ligand :
1s3s_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:62.81 %
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
42.7063-33.331817.1839


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
N6OGLY- 2073.06142.8H-Bond
(Ligand Donor)
N1NGLY- 2073.03159.77H-Bond
(Protein Donor)
O3BNGLY- 2483.08159.68H-Bond
(Protein Donor)
O2BNGLY- 2502.78138.24H-Bond
(Protein Donor)
O3ANGLY- 2503.45144.14H-Bond
(Protein Donor)
O2BNZLYS- 2512.850Ionic
(Protein Cationic)
O2BNLYS- 2513.19173.02H-Bond
(Protein Donor)
O1BOG1THR- 2523167.73H-Bond
(Protein Donor)
O1BNTHR- 2523.2137.02H-Bond
(Protein Donor)
O1ANTHR- 2523.03129.37H-Bond
(Protein Donor)
O1ANLEU- 2532.99149.59H-Bond
(Protein Donor)
C2'CD1LEU- 2534.010Hydrophobic
O2'NE2HIS- 3843.02166.52H-Bond
(Ligand Donor)
C5'CBALA- 4093.760Hydrophobic
C1'CBALA- 4123.990Hydrophobic