Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

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PDB ID Mentions in PubMed Central

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.

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Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034.

(2008) J Synchrotron Radiat 15

PubMed: 18421139 | PubMedCentral: PMC2394794 | DOI: 10.1107/S0909049507064229

Moreover, in the bifunctional enzyme, the protease is auto-inhibited by binding the six C-terminal residues of the helicase domain as the P side product of the cis cleavage of the NS3-NS4A junction (P... B code 1cu1 ; Yao et al. , 1999 ▶ ).

Publication Year: 2008


High-resolution functional profiling of hepatitis C virus genome.

(2008) PLoS Pathog 4

PubMed: 18927624 | PubMedCentral: PMC2564836 | DOI: 10.1371/journal.ppat.1000182

(B) Ribbon and surface diagrams of HCV genotype 1 NS3 monomer are shown (PDB accession code 1CU1) [49] .

Publication Year: 2008


Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function.

(2012) Nat Chem Biol 8

PubMed: 23023261 | PubMedCentral: PMC3480716 | DOI: 10.1038/nchembio.1081

The ligand complexes were solved using 1CU1 as a search model 25 rebuilt using COOT and refined using refmac and autoBUSTER 41 - 43 .

Publication Year: 2012


NS3 protease from hepatitis C virus: biophysical studies on an intrinsically disordered protein domain.

(2013) Int J Mol Sci 14

PubMed: 23803659 | PubMedCentral: PMC3742187 | DOI: 10.3390/ijms140713282

Figure 2 ( A ) Full-length NS3 protein from hepatitis C virus (PDB code: 1CU1) [ 26 ].

Publication Year: 2013


Computational study on the inhibitor binding mode and allosteric regulation mechanism in hepatitis C virus NS3/4A protein.

(2014) PLoS One 9

PubMed: 24586263 | PubMedCentral: PMC3934852 | DOI: 10.1371/journal.pone.0087077

systems simulation time starting structure apo protein 100 ns X-ray structure of HCV NS3/4A protein (PDB ID code 1CU1) inhibitor bound protein 100 ns X-ray structure of HCV NS3/4A protein complexed wi... h inhibitor (PDB ID code 4B73) apo protein (truncated) 100 ns removal of the six C-terminal residues from apo protein inhibitor bound protein(truncated) 100 ns removal of the six C-terminal residues from protein complexed with inhibitor All the structures were then modeled by using the program LEaP embedded in AMBER10 [35] with the standard AMBER03 force field [36] for protein, including adding all missing hydrogen atoms of the protein.

The simulations of the X-ray crystal structure of 1CU1 [16] and 4B73 [11] were designed to prove the importance of the stability of an autoinhibited form of HCV NS3/4A protein by a small molecular binding at the novel allosteric site.

As shown in Table 1 , the truncated forms of HCV NS3/4A protein models were created by in silico removing the six C-terminal residues coordinates starting from above structures 1CU1 and 4B73.

Publication Year: 2014


Docking studies of Pakistani HCV NS3 helicase: a possible antiviral drug target.

(2014) PLoS One 9

PubMed: 25188400 | PubMedCentral: PMC4154687 | DOI: 10.1371/journal.pone.0106339

Based on the protein BLAST, the UniProtKB: C1KIT2 shared highest sequence identity (83%) and the total query coverage (89%)with X-Ray structure of HCV isolated from genotype 1 (PDB ID: 1CU1) which has... been elucidated at 2.50 A 0 [11] .

g004 Figure 4 Structures of HCV NS3 Helicase (A) Ribbon form of 1CU1 protein, (domain A; dark blue and domain B; purple) (B) crystal structure of helicase 1A1V.

Publication Year: 2014


Comparison of structural architecture of HCV NS3 genotype 1 versus Pakistani genotype 3a.

(2014) Biomed Res Int 2014

PubMed: 25401105 | PubMedCentral: PMC4221965 | DOI: 10.1155/2014/749254

Sequences of crystal structures having PDB ids 3O8B [ 14 ], 1CU1 [ 15 ], 2ZJO [ 16 ], 1A1V [ 17 ], 1HEI [ 18 ], 2F55 [ 20 ], and 8OHM [ 21 ] were the other entries for NS3 protein in PDB and studied f... r protein-protein comparison.

The further analysis was done based on highest sequence identity and smallest distance from PK-NCVI/Pk3a as potential templates with comparative modeling, including PDB Ids 3KQN [ 19 ] (X-ray structure of hepatitis C virus NS3 helicase in complex with ssRNA), 3O8B [ 14 ] (Crystal structure of HCV NS3 protein), and 1CU1 [ 15 ].

Several crystal structures of HCV NS3 including PDB IDs 3O8B [ 14 ], 1CU1 [ 15 ], 2ZJO [ 16 ], 1A1V [ 17 ], 1HEI [ 18 ], 3KQN [ 19 ], 2F55 [ 20 ], and 8OHM [ 21 ] and mechanistic studies [ 12 , 21 – 27 ] helped to predict the ATP derived energy coupled helicase activity but all of the studies exclusively focused on genotype 1a or 1b of HCV.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4361677

The figure was generated using Pymol version 1.10 and the coordinates of PDB code 1CU1 [ 30 ].

The figure was generated using Pymol version 1.10 and the coordinates of PDB code 1CU1 [ 31 ].

Publication Year: 2015


Molecular models of NS3 protease variants of the Hepatitis C virus.

(2005) BMC Struct Biol 5

PubMed: 15663787 | PubMedCentral: PMC547903 | DOI: 10.1186/1472-6807-5-1

Results and discussion Primary sequence comparasion The identity between the sequences of a bifunctional protease structure (PDB access codes:1CU1, 1DY9) [ 31 , 38 ] (templates) and NS3 protease varia... ts (targets) is shown in Table 1 .

Quality of the models The atomic coordinates of crystallographic structure 1CU1 solved to resolution of the 2.5 Å were used as starting model for modeling of the NS3 protease variant structures, and the structure of NS3 complexed with an inhibitor (PDB access code: 1DY9) was used to generate homology models for docking studies.

There are two homology models for each sequence in the database, one obtained using 1CU1 as template and other using 1DY9 as template.

The sequence from crystallographic structure 1CU1 shows more than 79.1% identity with the sequences of NS3 protease variants, which provide high accuracy for the models (Table 1 ).

The analysis of the Ramachandran diagram φ-ψ plots of the 1CU1 structure (template) were used to compare the overall stereochemical quality of the NS3 protease variants structures against template solved by biocrystallography (Table 1 ).

Results The atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures.

The same analysis for crystallographic structure (1CU1) present 88.9% of residues in the most favorable, 10.5% additional allowed regions, 0.6% generously allowed regions, and 0.0% disallowed regions, which strongly indicates that the molecular models present good overall stereochemical quality.

The same analysis for crystallographic structure (1CU1) present rmsd values of the 0.013Å bond lengths and 1.67°, the average G-fator values of the 0.14 torsion angles and 0.28 covalent geometry, and Verify 3D values of the 321.53 score total and 1.09S quality.

Publication Year: 2005