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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:

4kh0

2.250 Å

X-ray

2013-04-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002}
ID:E8Y329_ECOKO
AC:E8Y329
Organism:Escherichia coli
Reign:Bacteria
TaxID:595495
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B34 %
D66 %


Ligand binding site composition:

B-Factor:79.033
Number of residues:30
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 3
Water Molecules: 1
Cofactors: ATP ATP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.395516.375

% Hydrophobic% Polar
38.5661.44
According to VolSite

Ligand :
4kh0_6 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:55.7 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
23.40189.15340.8191


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
O1GNE2HIS- 202.95166.96H-Bond
(Protein Donor)
C1'CD1LEU- 483.860Hydrophobic
C4'CGPRO- 494.080Hydrophobic
O3GOGSER- 502.54160.51H-Bond
(Protein Donor)
O2GNGLU- 522.95152.13H-Bond
(Protein Donor)
O1GNZLYS- 563.940Ionic
(Protein Cationic)
O3GNZLYS- 563.170Ionic
(Protein Cationic)
O3GNZLYS- 563.17163.01H-Bond
(Protein Donor)
O3ANZLYS- 563.05125.89H-Bond
(Protein Donor)
O1AO2'ATP- 2023.5164.6H-Bond
(Protein Donor)
O1AO3'ATP- 2022.76156.1H-Bond
(Protein Donor)
O1GMG MG- 2041.990Metal Acceptor
O2BMG MG- 2042.080Metal Acceptor