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PDB ID Mentions in PubMed Central Article count: 13

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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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Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance?

(2006) PLoS Pathog 2

PubMed: 16485036 | PubMedCentral: PMC1364504 | DOI: 10.1371/journal.ppat.0020010

Figure 8 Superposition of HIV-1 RT and HIV-2 RT Showing the Possible Effects of a Phe116Tyr Mutation Unliganded HIV-2 RT (PDB code 1MU2) is shown in yellow, unliganded HIV-1RT (PDB code 1DLO) is shown... in cyan, and HIV-1 RT/DNA/dTTP (PDB code 1RTD) is shown in red.

Publication Year: 2006

Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.

(2008) Nucleic Acids Res 36

PubMed: 18676450 | PubMedCentral: PMC2528191 | DOI: 10.1093/nar/gkn464

Superposition of the p51 subunit and the connection-RNase H domains of p66 for apo-RT69A, 1HNV and 1DLO structures results in a RMSD of 1.83 and 1.24 Å, respectively, with the major conformati... nal differences in all three structures between the fingers and thumb subdomains ( Supplementary Figure 4 ).

The crystal structure of apo-RT69A was solved by molecular replacement using apo-RT structure [PDB ID 1DLO ( 19 )] as the starting model.

Like the previously determined apo-RT structures [PDB ID: 1DLO ( 19 ), 1HNV ( 27 )], apo-RT69A contains no NNRTI-binding pocket and has the thumb and fingers subdomains in a closed conformation.

Publication Year: 2008

HIV reverse transcriptase: structural interpretation of drug resistant genetic variants from India.

(2009) Bioinformation 4

PubMed: 20011151 | PubMedCentral: PMC2770369 | DOI: null

The protein databank codes of the crystal structures of bound and unbound forms of RT used in this study are 1IKW [ 6 ], 1VRT [ 7 ], 1DLO [ 8 ], 1HMV [ 9 ], 1RTJ [ 10 ] and 1RTD [ 11 ].

Figure 2 (A) Location of M230 (green) in Efavirenz (in orange) bound RT (1IKW) Interactions involving M230 in unliganded RT structures (B) 1DLO and (C) 1RTJ.

(B-F) Local hydrogen bond interactions involving K101 in unliganded RT structure 1DLO,1HMV,1RTD, 1RTJ and in Nevirapine bound RT 1VRT (G) Structural superposition of 1IKW (yellow) and 1RTJ (green) showing changes in residue conformations.

In the ligand unbound RT structure, the side chain of Tyr 181 points into the hydrophobic pocket where the NNRTIs bind ( Figure 1B-1E ) This conformation is stabilized by the hydrogen bonds formed by the side chain hydroxyl group of Tyr 181 with the side chain N-H group of Asn 136 of the p55 subunit (1DLO, IRTD) and with side chain carboxyl of Glu 138 of the p55 subunit (1HMV) ( Figure 1B-D ).

M230L The position of M230L mutation site in Efavirenz bound RT structure is shown in Figure 2A In the ligand unbound RT structures in the closed conformation (1DLO,1HMV), Met 230 interacts with the side chain of Pro 95 through van der Waals forces ( Figure 2B ).

Publication Year: 2009

Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.

(2010) Viruses 2

PubMed: 20376302 | PubMedCentral: PMC2850067 | DOI: 10.3390/v2020606

This figure also shows that the loss of interaction due to Y181C mutation is compensated by the interaction between cyanovinyl group and conserved Y183 (based on structures from pdb codes: 1dlo, 2zd1 ... nd 3bgr).

Publication Year: 2010

Predictive power of molecular dynamics receptor structures in virtual screening.

(2011) J Chem Inf Model 51

PubMed: 21534609 | PubMedCentral: PMC3124922 | DOI: 10.1021/ci200117n

( 39 ) The four different systems included two bound systems, 1VRT ( 40 ) structure with α-APA bound to NNIBP (α-APA bound) and 1VRT structure with UC-781 bound to NNIBP (UC-781 bound)... as well as two unbound systems, 1VRT structure with the NNRTI extracted from NNIBP (unbound open) and 1DLO structure( 41 ) (unbound closed).

Publication Year: 2011

HIV-1 RT Inhibitors with a Novel Mechanism of Action: NNRTIs that Compete with the Nucleotide Substrate.

(2010) Viruses 2

PubMed: 21994659 | PubMedCentral: PMC3185657 | DOI: 10.3390/v2040880

Detailed view of the DAVP-1 binding pocket showing a superposition of the cα backbone in unliganded HIV-1 RT structures (in grey, PDB 1DLO, 1QE1 and 1HQE) and in RT bound to DAVP-1 (in orange,... PDB 3ITH and 3ISN).

Publication Year: 2010

Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme.

(2012) Bioinformation 8

PubMed: 23055609 | PubMedCentral: PMC3449371 | DOI: 10.6026/97320630008678

Methodology Protein selection and preparation : The PDB structure of unliganded HIV-1 RT (PDB ID=1DLO) at 2.7 Å resolution [ 39 ] was retrieved from the Research Collaboratory for Structural B... oinformatics (RCSB) Protein Data Bank (PDB) (RCSB, ).

Discussion Active Site Identification : After getting the PDB (1DLO) structure from RCSB ( ) the possible binding sites of structure were searched using the CASTp server, PASS programme and Q-site finder also confirmed by extensive literature search.

Publication Year: 2012

A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity.

(2013) PLoS One 8

PubMed: 24098331 | PubMedCentral: PMC3788777 | DOI: 10.1371/journal.pone.0074078

The structures chosen contain HIV-1 RT bound to NVP (PDB: 1VRT), double stranded DNA (PDB: 2HMI), a hybrid RNA/DNA duplex based on the polypurine tract (PDB: 1HYS) and the apo enzyme (PDB: 1DLO).

Publication Year: 2013

Selective unfolding of one Ribonuclease H domain of HIV reverse transcriptase is linked to homodimer formation.

(2014) Nucleic Acids Res 42

PubMed: 24574528 | PubMedCentral: PMC4005681 | DOI: 10.1093/nar/gku143

Simulated SAXS-scattering curves were generated using the p66 subunit from an RT crystal structure (pdb: 1DLO), or using a model of the polymerase domain in a p51-type conformation linked to a variabl... positioned RH domain by residues derived from partial unfolding of the C-terminus of the connection domain.

Publication Year: 2014

Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors.

(2012) Biology (Basel) 1

PubMed: 24832224 | PubMedCentral: PMC4009785 | DOI: 10.3390/biology1020222

These were the 1DLO apo structure, the 1IKW EFV bound structure and 1VRT NVP bound structure.

Figure 3 Comparison of the first 15 ANM modes generated from the apo HIV-1 RT structure and those of the NVP and EFV bound enzyme using the 1DLO, 1RTH and 1FK9 crystal structures respectively.

Figure 1 The structure of the HIV-1 RT shown along the template/primer binding cleft in the ( a ) closed apo (based on the 1DLO crystal structure) and ( b ) open NNRTI bound conformation (based on the EFV bound 1IKW structure, the van der Waals surface of the drug is shown).

Publication Year: 2012

Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.

(2013) Biomolecules 3

PubMed: 24970195 | PubMedCentral: PMC4030976 | DOI: 10.3390/biom3040889

The structures of apo wild-type (WT) RT (left; PDB ID: 1DLO) and WT RT bound to efavirenz (right; PDB ID: 1FK9).

Publication Year: 2013

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4399722

The sequences of these two protein sets are full length i.e. containing the 99 positions of the PR, 560 positions for the RT. Identification of the accessible variant positions In order to define the ... ccessibility of the AAs to an external ligand (i.e. a potential drug), we computed the surface accessible to the solvent, using the ASA software [ 26 ] available at RPBS [ 27 ], based on the 3D PR structure PDB ID:1HSG [ 28 ] and 3D RT structure PDB ID:1DLO [ 29 ].

We filtered the results of this exploration to keep only the pairs located on the protein surface as it is the most accessible location for known therapeutic targets (accessibility threshold greater than 25%, using the ASA software [ 26 ] and implemented by Allan et al. [ 27 ] based on the 3D PR structure PDB ID:1HSG [ 28 ] and 3D RT structure PDB ID:1DLO [ 29 ]).

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4452869

Additional time-dependent molecular dynamics simulations of the isolated fingers/palm domains starting from a structure that includes palm loop residues 219–230 (1S9E, green), the p51∆... L monomer in which palm loop residues from the 1DLO p66 subunit have been added back (4KSE, red), or the p51∆PL monomer taken to include the first 236 residues (corresponding to residues 1–249, since the construct is missing residues 219–230) (4KSE, black).

The δ-methyl-δ-methyl distances relative to the mutated residue based on structure 1DLO are also shown.

A structural comparison of the fingers/palm in an isolated construct (RT216, pdb: 1HAR) ( Unge et al., 1994 ), the p51∆PL monomer (pdb: 4KSE) ( Zheng et al., 2014 ), the p51 and p66 subunits of RT (pdb: 1DLO) ( Hsiou et al., 1996 ) reveals significant differences.

( B ) Ribbon diagram of the p66 subunit of RT (pdb: 1DLO) showing a portion of the fingers/palm domains (green) interacting with palm loop residues (219–230, magenta) of the palm domain.

Additional files Major datasets The following previously published datasets were used: Hsiou Y , Ding J , Das K , Clark Jr.

( C ) Ribbon representation of the p51/p51' homodimer derived from the p66/p51 heterodimer structure (pdb: 1DLO) by deletion of the p66 RH domain and replacement of the p51 subunit with the p51∆PL monomer.

AD , Hughes SH , Arnold E , 1996 , Human immunodeficiency virus type 1 , , Publicly available at RCSB Protein Data Bank (1DLO).

Based on pdb files 1DLO and 4KSE.

In the heterodimer structure, pdb: 1DLO ( Hsiou et al., 1996 ), the Ile382 δ-methyl is positioned 5.6 Å from the sidechain carbonyl oxygen of Asn136 on the p51 subunit.

( A ) Overlay of ribbon diagrams for fingers/palm residues 1–216 RT216 (pdb: 1HAR, gray) and in the p66 subunit of RT (pdb: 1DLO, fingers, teal; palm, orange).

Starting structures included residues 1–236 for the p66 and p51 subunits of apo RT (pdb: 1DLO).

Molecular dynamics simulations Molecular dynamics simulations were performed on the isolated fingers/palm domain, defined to include residues 1–236, starting with either subunit of the RT heterodimer, pdb: 1DLO ( Hsiou et al., 1996 ).

( B ) Overlay of ribbon diagrams for the fingers/palm in the p51∆PL monomer (pdb: 4KSE, gray) with the corresponding region of the p51 subunit of RT (pdb: 1DLO, fingers, teal; palm, orange).

The simulations utilized residues 1–236 in the p66 and p51 subunits of RT (pdb: 1DLO) after removing all other domains at t = 0, and the missing palm loop residues in the p51 starting structure were introduced as indicated in ‘Materials and methods’.

Publication Year: 2015