Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1xyv

1.790 Å

X-ray

2004-11-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Flavodoxin
ID:FLAV_DESVH
AC:P00323
Organism:Desulfovibrio vulgaris
Reign:Bacteria
TaxID:882
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.097
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.202270.000

% Hydrophobic% Polar
46.2553.75
According to VolSite

Ligand :
1xyv_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:67.1 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-10.755427.3611-21.7877


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
O2POGSER- 103.07134.66H-Bond
(Protein Donor)
O3POGSER- 102.69145.28H-Bond
(Protein Donor)
O1PNTHR- 112.6169.21H-Bond
(Protein Donor)
O2POG1THR- 122.77167.5H-Bond
(Protein Donor)
O2PNTHR- 122.86142.89H-Bond
(Protein Donor)
O4'ND2ASN- 142.71159.64H-Bond
(Protein Donor)
O2PNASN- 142.73162.35H-Bond
(Protein Donor)
C5'CBASN- 144.430Hydrophobic
O3POG1THR- 152.85150.39H-Bond
(Protein Donor)
O3PNTHR- 152.86161.88H-Bond
(Protein Donor)
O3POGSER- 583.43133.06H-Bond
(Protein Donor)
C5'CBSER- 583.620Hydrophobic
O2'OTHR- 592.62156.5H-Bond
(Ligand Donor)
C7MCE3TRP- 604.470Hydrophobic
C8MCZ3TRP- 603.590Hydrophobic
C2'CZ2TRP- 604.460Hydrophobic
C5'CZ2TRP- 603.910Hydrophobic
C4'CBCYS- 933.660Hydrophobic
N1NASP- 953.06125.4H-Bond
(Protein Donor)
O2NASP- 952.81156.59H-Bond
(Protein Donor)
C1'CBASP- 954.070Hydrophobic
C1'CE2TYR- 984.150Hydrophobic
N3OTYR- 1003172.19H-Bond
(Ligand Donor)
O2NCYS- 1022.64173.48H-Bond
(Protein Donor)
O4OHOH- 1652.64179.97H-Bond
(Protein Donor)