Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1pvo

3.000 Å

X-ray

2003-06-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Transcription termination factor Rho
ID:RHO_ECOLI
AC:P0AG30
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.6.4


Chains:

Chain Name:Percentage of Residues
within binding site
E17 %
F83 %


Ligand binding site composition:

B-Factor:53.185
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.138587.250

% Hydrophobic% Polar
51.1548.85
According to VolSite

Ligand :
1pvo_6 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:42.94 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
48.2843-6.1991948.2324


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
O1BNALA- 1823.41168.1H-Bond
(Protein Donor)
O1BNGLY- 1833.45131.18H-Bond
(Protein Donor)
O3ANGLY- 1833.47150.52H-Bond
(Protein Donor)
O1BNLYS- 1843.15150.57H-Bond
(Protein Donor)
O2BNTHR- 1852.57159.96H-Bond
(Protein Donor)
C1'SDMET- 1864.330Hydrophobic
C1'CZPHE- 3553.440Hydrophobic
DuArDuArPHE- 3553.940Aromatic Face/Face
O3GNH2ARG- 3663.02166.31H-Bond
(Protein Donor)
O3GCZARG- 3663.710Ionic
(Protein Cationic)