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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:

3wag

2.100 Å

X-ray

2013-05-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycosyltransferase
ID:Q76KZ6_STRHA
AC:Q76KZ6
Organism:Streptomyces halstedii
Reign:Bacteria
TaxID:1944
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:34.117
Number of residues:27
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.211864.000

% Hydrophobic% Polar
48.0551.95
According to VolSite

Ligand :
3wag_2 Structure
HET Code: TYD
Formula: C10H13N2O11P2
Molecular weight: 399.165 g/mol
DrugBank ID: DB03103
Buried Surface Area:55.85 %
Polar Surface area: 220.27 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-21.757837.01266.02468


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
O2AOGSER- 122.64142.18H-Bond
(Protein Donor)
C5'CD2TYR- 154.090Hydrophobic
C1'CBASN- 2303.990Hydrophobic
C5MCD1PHE- 3044.340Hydrophobic
N3OVAL- 3052.52175.93H-Bond
(Ligand Donor)
O4NVAL- 3053.07171.65H-Bond
(Protein Donor)
O2NLEU- 3072.86160.1H-Bond
(Protein Donor)
C2'CD2LEU- 3073.680Hydrophobic
O3BNGLY- 3242.91142.79H-Bond
(Protein Donor)
O3'OGLY- 3243.43130.04H-Bond
(Ligand Donor)
O2BNTHR- 3252.63154.33H-Bond
(Protein Donor)
O2BOG1THR- 3252.58151.14H-Bond
(Protein Donor)
O3'OD1ASN- 3283.42141.79H-Bond
(Ligand Donor)