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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:

1jdb

2.100 Å

X-ray

1997-03-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Carbamoyl-phosphate synthase large chain
ID:CARB_ECOLI
AC:P00968
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H100 %


Ligand binding site composition:

B-Factor:39.508
Number of residues:37
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 3
Water Molecules: 1
Cofactors:
Metals: MN MN K

Cavity properties

LigandabilityVolume (Å3)
0.119307.125

% Hydrophobic% Polar
57.1442.86
According to VolSite

Ligand :
1jdb_6 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:66.12 %
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
82.727285.259310.2361


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
O1ANH2ARG- 7143.01153.99H-Bond
(Protein Donor)
C5'CEMET- 7243.720Hydrophobic
N6OHIS- 7533.46130.83H-Bond
(Ligand Donor)
N1NLEU- 7553.21160.48H-Bond
(Protein Donor)
O3'OE2GLU- 7602.74163.89H-Bond
(Ligand Donor)
O2'OE1GLU- 7602.87170.88H-Bond
(Ligand Donor)
O2'NGLY- 7852.69152.42H-Bond
(Protein Donor)
O1BNE2HIS- 7873.21161.34H-Bond
(Protein Donor)
O3BNE2HIS- 7873.07132.73H-Bond
(Protein Donor)
O3'NSER- 7883.33155.47H-Bond
(Protein Donor)
O3BMN MN- 10792.360Metal Acceptor
O2AMN MN- 10792.170Metal Acceptor
O2BMN MN- 10802.670Metal Acceptor
O3BOHOH- 11222.98151.44H-Bond
(Protein Donor)