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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:

1y56

2.860 Å

X-ray

2004-12-02

Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein382aa long hypothetical sarcosine oxidase
ID:O59088_PYRHOO59089_PYRHO
AC:O59088O59089
Organism:Pyrococcus horikoshii
Reign:Archaea
TaxID:70601
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A33 %
B67 %


Ligand binding site composition:

B-Factor:33.801
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.849550.125

% Hydrophobic% Polar
55.2144.79
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1y56HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
1y56_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:63.5 %
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
112.38359.529224.5354
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1y56RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


Binding mode :
What is Poseview ?
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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
C5'CGARG- 464.350Hydrophobic
O1PNH2ARG- 463.01139.66H-Bond
(Protein Donor)
O1PNH1ARG- 463.18133.73H-Bond
(Protein Donor)
O1PCZARG- 463.510Ionic
(Protein Cationic)
C8CD1ILE- 2614.120Hydrophobic
C7CD1ILE- 2613.70Hydrophobic
O4'NH2ARG- 3023.2151.91H-Bond
(Protein Donor)
C1'CDARG- 30240Hydrophobic
C8MCZ2TRP- 3043.810Hydrophobic
C1'CE3TRP- 3043.470Hydrophobic
C3'CD2TRP- 3044.370Hydrophobic
C5'CBTRP- 3044.160Hydrophobic
C9CZ2TRP- 3043.290Hydrophobic
O2'NZLYS- 4373.4128.93H-Bond
(Protein Donor)
O3'NH1ARG- 4382.95129.47H-Bond
(Protein Donor)
N3OMET- 4443.38156.24H-Bond
(Ligand Donor)
O2NE2GLN- 4483.26176.65H-Bond
(Protein Donor)
O1PNEARG- 4773.48167.28H-Bond
(Protein Donor)
O5'OHOH- 8083.21179.96H-Bond
(Protein Donor)