Primary Citation PubMed: 21358046
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Computational interaction analysis of organophosphorus pesticides with different metabolic proteins in humans.
(2011) J Biomed Res 25
PubMed: 23554709 | PubMedCentral: PMC3596730 | DOI: 10.1016/S1674-8301(11)60045-6
D: Binding energy -36.57 of protein kinase C (Pdbid: 2XJ1) with azinphosmethyl.
Identified protein's Ligands with highest docked score Global energy Attractive Van der Wall force Repulsive Van der Wall force Atomic contact energy (ACE) Acetylcholinesterase (Pdbid: 3LII) Parathion -37.90 -15.66 2.83 -10.50 Cytochrome protein P450 (Pdbid: 3NXU) Phosmet -45.21 -14.83 2.32 -15.72 Gutathione S-transferase (Pdbid: 4GTU) Azinphosmethyl -39.60 -15.23 3.46 -13.37 Protein kinase C (Pdbid: 2XJ1) Azinphosmethyl -36.57 -13.71 1.49 -11.03 Anti-chymotrypsin (Pdbid: 1YXA) Quinalphos -30.15 -14.07 0.77 -7.62 The highest interaction energy of all five proteins like acetylcholinesterase, cytochrome protein P450, gutathione S-transferase, protein kinase C and α-1-antichymotrypsin in H. sapiens with the top five different organophosphorous pesticides like parathion, phosmet, azinphosmethyl and quinalphos respectively that show the highest interaction with each other.
The third one is GST (4GTU), which has 2 pairs of anti-parallel β-sheets and eight α-helices, and the fourth is the PKC (2XJ1), which has 12 mixed β-sheets and 13 α-helices.
We accessed the tertiary structures from PDB with the proposed interaction of five different human proteins like AchE (3LII), cytochrome P450 (3NXU), GST (4GTU), PKC (2XJ1) and α1-antichymotrypsin (1YXA) with these organophosphorus pesticides by using these tools.
The crystal structure of five different proteins, PDBIDs: 3LII, 3NXU, 4GTU, 2XJ1 and 1YXA in Homo sapiens ( H. sapiens ), interact with organophosphorus pesticides at the molecular level.
Various methods applied in this study are given below Preparation of proteins The crystal structures of AchE, P450, GST, PKC, and ACT and their PDBID, 3LII, 3NXU, 4GTU, 2XJ1, and 1YXA  –  were downloaded from the PDB in *.
Table 1 Ramachandran map of AChE, P450, GST, PKC and ACT proteins there PDBIDs are 3LII, 3NXU, 4GTU, 2XJ1 and 1YXA respectively were calculated with the PROCHECK program Model Description 3LII 3NXU 4GTU 2XJ1 1YXA Residues in most favoured regions [A,B,L] 358/82.1% 356/90.4% 217/91.4% 224/94.1% 308/91.7% Residues in additional allowed regions [a,b,l,p] 71/16.3% 36/9.1% 8/4.0% 12/5.0% 28/8.3% Residues in generously allowed regions [∼a,∼b,∼l,∼p] 4/0.9% 1/0.3% 1/0.6% 1/0.4% 0/0.0% Residues in disallowed regions 3/0.7% 1/0.3% 3/0.7% 1/0.4% 0/0.0% ERRAT overall quality score 87.833 97.105 90.431 97.619 98.256 VERIFY 3-D (3D-1D score > 0.2) 97.76% 96.29% 95.54% 98.54% 94.10% ProSA Z-score -10.62 -9.84 -8.93 -7.63 -8.64 SCOP (Domains) Region: 3-530 Region: 5-457 Region: 85-216 Region: 4-263 Region: 1-371 Region: 2-84 The Z-score and ERRAT overall quality score by servers like ERRAT and SUPERFAMILY sequence search server.
In conclusion, the analysis of docking with ten organophosphorus pesticides with five target proteins (their PDBID are 3LII, 3NXU, 4GTU, 2XJ1 and 1YXA) in H. sapiens highlighted some important interactions operating at the molecular level and caused toxicity in the human body.
Hence, this research hypothesis focuses on a comparison and interaction study of five different metabolic and physiological proteins [PDBIDs: 3LII, 3NXU, 4GTU, 2XJ1 and 1YXA in Homo sapiens ( H. sapiens )], which are inhibited by the exposure to ten different organophosphorus pesticides and exert their toxic effects on humans metabolism, by using online bioinformatics tools and softwares.
The protein kinase pim-1 in complex with a small molecule inhibitor (PDBID: 2XJ1)  has a 2.13 Å resolution and serpina3n, a murine orthologue of human α1-antichymotrypsin (PDBID: 1YXA)  has a 2.10 Å resolution.
The overall model quality of all five 3-D structures was reflected by the minimum Z-score, which was -7.63 for PKC (PDBID: 2XJ1) and the maximum Z-score, which was -10.62 for AchE (PDBID: 3LII) as is shown in Table 1 .
Publication Year: 2011
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.