Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3vuf

3.000 Å

X-ray

2012-06-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Granule-bound starch synthase 1, chloroplastic/amyloplastic
ID:SSG1_ORYSJ
AC:Q0DEV5
Organism:Oryza sativa subsp. japonica
Reign:Eukaryota
TaxID:39947
EC Number:2.4.1.242


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:68.427
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.851999.000

% Hydrophobic% Polar
48.9951.01
According to VolSite

Ligand :
3vuf_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:54.14 %
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
-55.9538-9.4131937.707


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O2BNGLY- 1003.13127.87H-Bond
(Protein Donor)
O3BNEARG- 4083.49134.46H-Bond
(Protein Donor)
O3BNH2ARG- 4082.84170.57H-Bond
(Protein Donor)
O3BCZARG- 4083.60Ionic
(Protein Cationic)
C5'CGARG- 4084.160Hydrophobic
O5'NZLYS- 4132.84161.55H-Bond
(Protein Donor)
C2'CD1ILE- 4903.470Hydrophobic
O2'OE1GLN- 4933.17144.5H-Bond
(Ligand Donor)