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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:

3sgl

2.700 Å

X-ray

2011-06-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
ID:MNMC_YERPE
AC:Q8ZD36
Organism:Yersinia pestis
Reign:Bacteria
TaxID:632
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.614
Number of residues:70
Including
Standard Amino Acids: 64
Non Standard Amino Acids: 1
Water Molecules: 5
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.9681586.250

% Hydrophobic% Polar
41.4958.51
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3sglHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3sgl_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:72.79 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
8.168744.451530.488472
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3sglRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.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
C4'CG2ILE- 2744.30Hydrophobic
O1PNVAL- 2753.22161.74H-Bond
(Protein Donor)
N3ANALA- 2952.92139.19H-Bond
(Protein Donor)
O1ANALA- 3032.65158.11H-Bond
(Protein Donor)
O2ANALA- 3033.45123.51H-Bond
(Protein Donor)
C8MCBALA- 3034.20Hydrophobic
C3'CBALA- 3034.420Hydrophobic
O2AOGSER- 3042.56159.66H-Bond
(Protein Donor)
O4'OGSER- 3043.24148.22H-Bond
(Ligand Donor)
N3OALA- 3102.78161.59H-Bond
(Ligand Donor)
O4NALA- 3102.99147.9H-Bond
(Protein Donor)
N6AOLEU- 4353.46154.87H-Bond
(Ligand Donor)
N1ANLEU- 4352.88157.87H-Bond
(Protein Donor)
C1BCG2THR- 4654.480Hydrophobic
C7MCG2VAL- 4873.510Hydrophobic
C7MCBALA- 5234.040Hydrophobic
C8CGARG- 5713.920Hydrophobic
C4'CBLEU- 6274.420Hydrophobic
C5'CD1LEU- 6273.970Hydrophobic
O3'OGLY- 6282.68145.38H-Bond
(Ligand Donor)
O2'NGLY- 6312.6134.75H-Bond
(Protein Donor)
O2NLEU- 6322.62133.46H-Bond
(Protein Donor)
O2POHOH- 7152.81179.98H-Bond
(Protein Donor)
O3BOHOH- 7343.14163.39H-Bond
(Ligand Donor)
O1POHOH- 7352.95179.97H-Bond
(Protein Donor)
O1AOHOH- 7372.78179.97H-Bond
(Protein Donor)
O2POHOH- 7522.87163.13H-Bond
(Protein Donor)