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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:

3b1x

2.610 Å

X-ray

2011-07-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ferrous iron transport protein B
ID:Q5M586_STRT2
AC:Q5M586
Organism:Streptococcus thermophilus
Reign:Bacteria
TaxID:264199
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:20.523
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.715411.750

% Hydrophobic% Polar
47.5452.46
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3b1xHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
3b1x_2 Structure
HET Code: GNP
Formula: C10H13N6O13P3
Molecular weight: 518.164 g/mol
DrugBank ID: DB02082
Buried Surface Area:74.28 %
Polar Surface area: 338.36 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-32.347419.3426-46.6078
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3b1xRingsAromatic 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
O1BNSER- 123.3141.69H-Bond
(Protein Donor)
O1BNGLY- 133.13142.51H-Bond
(Protein Donor)
O3ANGLY- 133.01131.88H-Bond
(Protein Donor)
O1GNZLYS- 142.75149.76H-Bond
(Protein Donor)
O1BNLYS- 143.11166.97H-Bond
(Protein Donor)
O1BNZLYS- 142.71137.51H-Bond
(Protein Donor)
O1GNZLYS- 142.750Ionic
(Protein Cationic)
O1BNZLYS- 142.710Ionic
(Protein Cationic)
O2BNTHR- 153.18162.51H-Bond
(Protein Donor)
O1ANSER- 162.97141.15H-Bond
(Protein Donor)
O1AOGSER- 162.7169.96H-Bond
(Protein Donor)
C2'CG1VAL- 283.760Hydrophobic
O2ANGLY- 293.28159.58H-Bond
(Protein Donor)
C3'CBASN- 304.330Hydrophobic
O2GNGLY- 332.79127.49H-Bond
(Protein Donor)
O2GNVAL- 342.76143.88H-Bond
(Protein Donor)
O3GNTHR- 352.83161.71H-Bond
(Protein Donor)
N7ND2ASN- 1133.29136.25H-Bond
(Protein Donor)
C4'CEMET- 1144.460Hydrophobic
C1'CEMET- 1144.170Hydrophobic
O6NMET- 1143.35128.45H-Bond
(Protein Donor)
N1OD1ASP- 1162.64164.85H-Bond
(Ligand Donor)
N1OD2ASP- 1163.33128.55H-Bond
(Ligand Donor)
N2OD2ASP- 1162.77157.32H-Bond
(Ligand Donor)
O6OGSER- 1423.43160.66H-Bond
(Protein Donor)
O6NALA- 1432.78151.78H-Bond
(Protein Donor)
O3GMG MG- 3011.970Metal Acceptor
O2BMG MG- 3011.940Metal Acceptor