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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:

3umo

1.700 Å

X-ray

2011-11-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:ATP-dependent 6-phosphofructokinase isozyme 2
ID:PFKB_ECOLI
AC:P06999
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:2.7.1.11


Chains:

Chain Name:Percentage of Residues
within binding site
A95 %
B5 %


Ligand binding site composition:

B-Factor:22.265
Number of residues:43
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 3
Water Molecules: 2
Cofactors: ATP
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.8971542.375

% Hydrophobic% Polar
39.6160.39
According to VolSite

Ligand :
3umo_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:68.73 %
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
6.22713-20.218913.3105


Binding mode :
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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
O1GNZLYS- 273.13176.31H-Bond
(Protein Donor)
O1GNZLYS- 273.130Ionic
(Protein Cationic)
O3GNZLYS- 273.240Ionic
(Protein Cationic)
O2BNZLYS- 1852.87165.22H-Bond
(Protein Donor)
O2BNZLYS- 1852.870Ionic
(Protein Cationic)
O1BND2ASN- 1872.97171.34H-Bond
(Protein Donor)
O2AOGSER- 2242.84128.47H-Bond
(Protein Donor)
O3AOGSER- 2243.09158.71H-Bond
(Protein Donor)
C5'CBSER- 2244.030Hydrophobic
O2ANGLY- 2262.77155.32H-Bond
(Protein Donor)
O3'OGLY- 2292.71138.78H-Bond
(Ligand Donor)
C2'CGPRO- 2434.480Hydrophobic
C1'CBALA- 2544.210Hydrophobic
C5'CBALA- 2544.020Hydrophobic
O2GNGLY- 2553.14153.18H-Bond
(Protein Donor)
C5'SDMET- 2583.960Hydrophobic
C4'CEMET- 2583.870Hydrophobic
O2'OGSER- 2843.04159.04H-Bond
(Ligand Donor)
C1'CBSER- 2844.280Hydrophobic
N3OGSER- 2842.95173.46H-Bond
(Protein Donor)
C1'CG2THR- 2874.470Hydrophobic
O1GMG MG- 3102.140Metal Acceptor
O2BMG MG- 3102.050Metal Acceptor
O3GMG MG- 3112.130Metal Acceptor
O1BMG MG- 3112.060Metal Acceptor