Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1mjt

2.400 Å

X-ray

2002-08-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nitric oxide synthase oxygenase
ID:NOSO_STAAU
AC:P0A004
Organism:Staphylococcus aureus
Reign:Bacteria
TaxID:1280
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A55 %
B45 %


Ligand binding site composition:

B-Factor:34.345
Number of residues:23
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 2
Water Molecules: 3
Cofactors: NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0281336.500

% Hydrophobic% Polar
46.2153.79
According to VolSite

Ligand :
1mjt_3 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:47.28 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
23.951793.727837.893


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
O1ANZLYS- 3133.920Ionic
(Protein Cationic)
O5BNZLYS- 3132.940Ionic
(Protein Cationic)
O1NNZLYS- 3133.540Ionic
(Protein Cationic)
O5BNZLYS- 3132.94148.33H-Bond
(Protein Donor)
C5DCD2TRP- 3143.580Hydrophobic
C2DCZ2TRP- 3144.020Hydrophobic
C3DCE2TRP- 3143.70Hydrophobic
O1NOGSER- 3153.12160.12H-Bond
(Protein Donor)
C5DCBSER- 3153.70Hydrophobic
O2DOTYR- 3293.1144H-Bond
(Ligand Donor)
O3OHOH- 12003.36179.97H-Bond
(Protein Donor)