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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:

3t2g

3.000 Å

X-ray

2011-07-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Fructose-1,6-bisphosphate aldolase/phosphatase
ID:B1YAL1_PYRNV
AC:B1YAL1
Organism:Pyrobaculum neutrophilum
Reign:Archaea
TaxID:444157
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:37.678
Number of residues:24
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 3
Water Molecules: 0
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.498789.750

% Hydrophobic% Polar
38.0361.97
According to VolSite

Ligand :
3t2g_1 Structure
HET Code: 13P
Formula: C3H5O6P
Molecular weight: 168.042 g/mol
DrugBank ID: DB04326
Buried Surface Area:71.39 %
Polar Surface area: 119.53 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-62.047728.787417.7256


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
C3CBHIS- 184.210Hydrophobic
O2PNZLYS- 1332.85130.88H-Bond
(Protein Donor)
O2PNZLYS- 1332.850Ionic
(Protein Cationic)
O3NARG- 2662.74166H-Bond
(Protein Donor)
O3OD2ASP- 2972.93162.31H-Bond
(Ligand Donor)
O2PMG MG- 4082.030Metal Acceptor
O3PMG MG- 4092.410Metal Acceptor