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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:

1q19

2.400 Å

X-ray

2003-07-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Carbapenam-3-carboxylate synthase
ID:CARA_PECCC
AC:Q9XB61
Organism:Pectobacterium carotovorum subsp. carotovorum
Reign:Bacteria
TaxID:555
EC Number:6.3.3.6


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:27.675
Number of residues:19
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.384408.375

% Hydrophobic% Polar
47.9352.07
According to VolSite

Ligand :
1q19_4 Structure
HET Code: SSC
Formula: C7H10NO4
Molecular weight: 172.159 g/mol
DrugBank ID: DB03215
Buried Surface Area:52.86 %
Polar Surface area: 96.87 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 1
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-8.99158-5.743517.6827


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
C3SCD1ILE- 3233.560Hydrophobic
CSSCZTYR- 3453.610Hydrophobic
O1SNGLY- 3463.21129.08H-Bond
(Protein Donor)
O2SNGLY- 3463.14161.53H-Bond
(Protein Donor)
O1SNASP- 3483.5140.7H-Bond
(Protein Donor)
C5SCD2LEU- 3494.140Hydrophobic
C5SCG2ILE- 3544.270Hydrophobic