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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:

2zdg

2.200 Å

X-ray

2007-11-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:D-alanine--D-alanine ligase
ID:DDL_THET8
AC:Q5SHZ3
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:43.235
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.388860.625

% Hydrophobic% Polar
37.6562.35
According to VolSite

Ligand :
2zdg_2 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:59.27 %
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
22.361968.672529.1616


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
O3BNZLYS- 1163138.93H-Bond
(Protein Donor)
O1ANZLYS- 1163.22159H-Bond
(Protein Donor)
O3BNZLYS- 11630Ionic
(Protein Cationic)
O1ANZLYS- 1163.220Ionic
(Protein Cationic)
C1'CE2PHE- 1513.480Hydrophobic
DuArDuArPHE- 1513.910Aromatic Face/Face
O1ANZLYS- 1533.02149.67H-Bond
(Protein Donor)
N7NZLYS- 1533.09176.85H-Bond
(Protein Donor)
O1ANZLYS- 1533.020Ionic
(Protein Cationic)
O1BNSER- 1602.85129.25H-Bond
(Protein Donor)
C5'CBSER- 1604.050Hydrophobic
C5'CD1ILE- 1633.850Hydrophobic
N6OE1GLU- 1893.15170.31H-Bond
(Ligand Donor)
N6OLYS- 1902.89134.36H-Bond
(Ligand Donor)
N1NLEU- 1922.62165.84H-Bond
(Protein Donor)
O3'OE1GLU- 1972.64166.27H-Bond
(Ligand Donor)
O3'OE2GLU- 1973.49136.39H-Bond
(Ligand Donor)
O2'OE1GLU- 1972.59159.78H-Bond
(Ligand Donor)
C3'CZPHE- 2724.160Hydrophobic
C2'CE1PHE- 2723.890Hydrophobic
C1'CZPHE- 2724.460Hydrophobic
O1AND2ASN- 2813.09176.49H-Bond
(Protein Donor)