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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:

2j6x

2.100 Å

X-ray

2006-10-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Lactate oxidase
ID:Q44467_9LACT
AC:Q44467
Organism:Aerococcus viridans
Reign:Bacteria
TaxID:1377
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H100 %


Ligand binding site composition:

B-Factor:9.400
Number of residues:44
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.024604.125

% Hydrophobic% Polar
41.9058.10
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2j6xHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2j6x_8 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:83.11 %
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
45.833117.57170.294
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2j6xRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


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
C7MCE2TYR- 403.830Hydrophobic
C7MCG1ILE- 414.110Hydrophobic
C3'CBALA- 923.930Hydrophobic
O2'OPRO- 932.82173.57H-Bond
(Ligand Donor)
C2'CG1ILE- 943.870Hydrophobic
C6CG2ILE- 943.510Hydrophobic
C9CG1ILE- 943.680Hydrophobic
N5NALA- 953.31157.67H-Bond
(Protein Donor)
O4OGSER- 1222.88140.68H-Bond
(Protein Donor)
N3OE1GLN- 1442.95162.04H-Bond
(Ligand Donor)
O2OG1THR- 1722.68158.55H-Bond
(Protein Donor)
O2NZLYS- 2412.81139.14H-Bond
(Protein Donor)
O2'NZLYS- 2412.88155.98H-Bond
(Protein Donor)
O3'OGSER- 2633.43131.81H-Bond
(Protein Donor)
C9CDARG- 2683.580Hydrophobic
O3'OD1ASP- 2963.23130.9H-Bond
(Ligand Donor)
O3'OD2ASP- 2962.67163.6H-Bond
(Ligand Donor)
C5'CBASP- 2964.310Hydrophobic
C5'CBSER- 2974.330Hydrophobic
O3PNGLY- 2983.09157.68H-Bond
(Protein Donor)
O2PCZARG- 3003.620Ionic
(Protein Cationic)
O3PCZARG- 3003.910Ionic
(Protein Cationic)
O2PNH2ARG- 3002.8173.5H-Bond
(Protein Donor)
O3PNH1ARG- 3003171.29H-Bond
(Protein Donor)
C8MCGARG- 3203.510Hydrophobic
O1PNARG- 3202.77167.03H-Bond
(Protein Donor)
O2PNH1ARG- 3202.69132.2H-Bond
(Protein Donor)
O2PCZARG- 3203.870Ionic
(Protein Cationic)
C7MCD2LEU- 3234.360Hydrophobic
O3POHOH- 21362.83158.63H-Bond
(Protein Donor)
O3POHOH- 21592.66132.44H-Bond
(Protein Donor)