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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:

4nh0

2.900 Å

X-ray

2013-11-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:ESX secretion system protein EccC
ID:D1A4G7_THECD
AC:D1A4G7
Organism:Thermomonospora curvata
Reign:Bacteria
TaxID:471852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:85.706
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.707297.000

% Hydrophobic% Polar
56.8243.18
According to VolSite

Ligand :
4nh0_2 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:53.3 %
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
-63.0823-11.981357.796


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
O1GNGLN- 8343.17172.45H-Bond
(Protein Donor)
O3BNGLN- 8343.42124.49H-Bond
(Protein Donor)
C5'CGGLN- 8344.060Hydrophobic
O2BNTHR- 8352.95140.32H-Bond
(Protein Donor)
O2BNGLY- 8363.3171.9H-Bond
(Protein Donor)
O3ANGLY- 8363.15122.8H-Bond
(Protein Donor)
O1GNZLYS- 8373.03122.54H-Bond
(Protein Donor)
O2BNZLYS- 8372.59147.97H-Bond
(Protein Donor)
O1GNZLYS- 8373.030Ionic
(Protein Cationic)
O2BNZLYS- 8372.590Ionic
(Protein Cationic)
O1BNSER- 8382.99151.35H-Bond
(Protein Donor)
O1AOG1THR- 8392.71168.53H-Bond
(Protein Donor)
O1ANTHR- 8392.6138.87H-Bond
(Protein Donor)
C1'CBPRO- 10183.90Hydrophobic
N6OG1THR- 10312.54138.71H-Bond
(Ligand Donor)
N6OTHR- 10312.62125.89H-Bond
(Ligand Donor)
O2GMG MG- 14022.060Metal Acceptor
O1BMG MG- 14022.670Metal Acceptor