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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:

5dm3

2.600 Å

X-ray

2015-09-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:L-glutamine synthetase
ID:Q1QZR8_CHRSD
AC:Q1QZR8
Organism:Chromohalobacter salexigens
Reign:Bacteria
TaxID:290398
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
E79 %
F21 %


Ligand binding site composition:

B-Factor:66.257
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7961491.750

% Hydrophobic% Polar
25.3474.66
According to VolSite

Ligand :
5dm3_5 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:53.95 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-52.222-45.301428.7869


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
O2BNZLYS- 363.970Ionic
(Protein Cationic)
O2BND1HIS- 522.88145.88H-Bond
(Protein Donor)
C1'CBALA- 1413.690Hydrophobic
O3'OE1GLU- 2013.31157.79H-Bond
(Ligand Donor)
O2'NCYS- 2182.89134.28H-Bond
(Protein Donor)
C1'CBCYS- 21840Hydrophobic
C1'CBHIS- 2644.450Hydrophobic
O5'NH2ARG- 3482.95123.03H-Bond
(Protein Donor)