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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:

3mhy

1.400 Å

X-ray

2010-04-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nitrogen regulatory protein P-II 1
ID:P70731_AZOBR
AC:P70731
Organism:Azospirillum brasilense
Reign:Bacteria
TaxID:192
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A56 %
C44 %


Ligand binding site composition:

B-Factor:18.802
Number of residues:40
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.504489.375

% Hydrophobic% Polar
54.4845.52
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3mhyHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
3mhy_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:81.03 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
0.28058117.08495.87471
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3mhyRingsAromatic 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
C4'CG2ILE- 73.760Hydrophobic
C1'CG2ILE- 74.010Hydrophobic
O2'OG1THR- 292.84154.18H-Bond
(Ligand Donor)
N3OG1THR- 292.89156.59H-Bond
(Protein Donor)
O1GNH1ARG- 382.91169.09H-Bond
(Protein Donor)
O1BNARG- 382.84150.35H-Bond
(Protein Donor)
O1GCZARG- 383.650Ionic
(Protein Cationic)
O1GNE2GLN- 393.04161.31H-Bond
(Protein Donor)
C4'CDLYS- 584.470Hydrophobic
N6OALA- 643.07163.22H-Bond
(Ligand Donor)
N1NALA- 642.91174.34H-Bond
(Protein Donor)
O2GNGLY- 872.86141.46H-Bond
(Protein Donor)
O2ANGLY- 892.79132.77H-Bond
(Protein Donor)
O2BNZLYS- 902.95138.85H-Bond
(Protein Donor)
N7NZLYS- 902.99160.84H-Bond
(Protein Donor)
O2BNZLYS- 902.950Ionic
(Protein Cationic)
O2BNEARG- 1013152.93H-Bond
(Protein Donor)
O2BNH2ARG- 1013.08144.71H-Bond
(Protein Donor)
O3BNEARG- 1013.21138.38H-Bond
(Protein Donor)
O2BCZARG- 1013.480Ionic
(Protein Cationic)
O1GCZARG- 1033.860Ionic
(Protein Cationic)
O3GCZARG- 1033.640Ionic
(Protein Cationic)
O1GNH2ARG- 1033.06172.52H-Bond
(Protein Donor)
O3GNEARG- 1032.79153.27H-Bond
(Protein Donor)
N6OLEU- 1123155.15H-Bond
(Ligand Donor)
O2GMG MG- 1152.030Metal Acceptor
O1BMG MG- 1152.080Metal Acceptor
O1AMG MG- 1152.070Metal Acceptor
O3GOHOH- 1232.8137.17H-Bond
(Protein Donor)
O2BOHOH- 2032.92179.96H-Bond
(Protein Donor)