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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:

3gtc

1.900 Å

X-ray

2009-03-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-lactamase
ID:AMPC_ECOLI
AC:P00811
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.5.2.6


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.275
Number of residues:19
Including
Standard Amino Acids: 18
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.242540.000

% Hydrophobic% Polar
27.5072.50
According to VolSite

Ligand :
3gtc_1 Structure
HET Code: GTC
Formula: C9H12N3O2S
Molecular weight: 226.275 g/mol
DrugBank ID: DB07850
Buried Surface Area:46.6 %
Polar Surface area: 108.64 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
20.47484.2697310.5689


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
S15CG2VAL- 2093.850Hydrophobic
C1CG2VAL- 2114.070Hydrophobic
N9NSER- 2122.94159.35H-Bond
(Protein Donor)
C2CGTYR- 2213.670Hydrophobic
C3CE2TYR- 2213.910Hydrophobic
C1CD1TYR- 2213.590Hydrophobic
C6CBTHR- 3194.160Hydrophobic
N11NGLY- 3202.52152.8H-Bond
(Protein Donor)