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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:

1r8c

1.900 Å

X-ray

2003-10-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:CCA-adding enzyme
ID:CCA_ARCFU
AC:O28126
Organism:Archaeoglobus fulgidus
Reign:Archaea
TaxID:224325
EC Number:2.7.7.72


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:31.766
Number of residues:36
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 3
Water Molecules: 1
Cofactors:
Metals: MN MN MN

Cavity properties

LigandabilityVolume (Å3)
1.0711258.875

% Hydrophobic% Polar
42.3657.64
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1r8cHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1r8c_1 Structure
HET Code: UTP
Formula: C9H11N2O15P3
Molecular weight: 480.109 g/mol
DrugBank ID: DB04005
Buried Surface Area:41.48 %
Polar Surface area: 299.67 Å2
Number of
H-Bond Acceptors: 15
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
16.001513.25234.3556
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1r8cRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.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
O2BNSER- 472.95151.6H-Bond
(Protein Donor)
O1GOGSER- 472.62169.67H-Bond
(Protein Donor)
C4'CG2THR- 1303.430Hydrophobic
O3'ND1HIS- 1333.49122.74H-Bond
(Protein Donor)
O1GNZLYS- 1523.34137.51H-Bond
(Protein Donor)
O1GNZLYS- 1523.340Ionic
(Protein Cationic)
O2GOHTYR- 1612.72126.27H-Bond
(Protein Donor)
O1AMN MN- 6002.310Metal Acceptor
O2BMN MN- 6002.090Metal Acceptor
O3GMN MN- 6002.310Metal Acceptor