Citations in PubMed

Primary Citation PubMed: 9837729 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers.

(2007) Nucleic Acids Res 35

PubMed: 17644816 | PubMedCentral: PMC1976467 | DOI: 10.1093/nar/gkm420

Overlaying these sites with a crystal structure of HIV-1 RT bound to a dsDNA primer-template [2HMI and 1RTD, ( 30 , 34 )] show this difference in intensities can be explained by the formation of a dou... le helix and that these regions would be solvent exposed if they bound RT as primer-template mimics ( Figure 9 A).

Publication Year: 2007

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

(2010) Viruses 2

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

The crystal structure of HIV-1 RT bound to double stranded DNA (PDB code 2hmi).

The RNA/DNA (panel A; PDB code 1hys) maintains the protein contacts seen in the complex with DNA/DNA (panel B, PDB code 2hmi) (these contacts are not shown in panel A. and has thirteen additional contacts.

Publication Year: 2010

Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation.

(2010) BMC Bioinformatics 11

PubMed: 20584304 | PubMedCentral: PMC2911459 | DOI: 10.1186/1471-2105-11-352

On the contrary, there were cases that had good results with RotBUS at 1% filtering, but not with FTDock, such as those with PDB code 1de4 , 1n2c , 2hmi , and 2qfw .

Some interesting examples are the cases with PDB code 1de4 , 1n2c and 2hmi , which had pyDock ranks between 12 and 32 when docking poses were generated by RotBUS, although they did not have any acceptable solution generated by FTDOCK.

Publication Year: 2010

Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

(2012) BMC Bioinformatics 13

PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165

Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH &#... 000a0;     Cro & repressor 1LMB   Homeodomain 1FJL, 1HDD, 6PAX   LacI repressor 1WET   Endonuclease Fok1 1FOK   Gamma Delta resolvase 1GDT   Hin recombinase 1HCR   RAP1 family 1IGN   Prd paired domain 1PDN   Tc3 transposase 1TC3   Trp repressor 1TRR   Diptheria tox repressor 1DDN   Transcription factor IIB 1D3U   Interferon regulatory 2IRF   Catabolite gene activator protein 1RUO   Transcription factor 1CF7, 3HTS   Ets domain 1BC8 Zinc Co-ordinating       β-β-α zinc finger 1ZAA   Harmone Nuclear Receptor 2NLL   Loop sheet helix 1TSR   GAL4 type 1ZME Zipper type       Leucine Zipper 1YSA   Helix loop helix 1AN2 Other-α Helix       Pappilomavirus 1 E2 2BOP   Histone 1AOI   EBNA1 nuclear protein 1B3T   Skn-1 transcription factor 1SKN   Cre Recombinase 1CRX   High Mobility Group 1QRV   MADS box 1MNM β-Sheet       TATA box binding 1YTB β-Hairpin/Ribbon       MetJ repressor 1CMA   Tus replication terminator 1ECR   Integration host factor 1IHF   Transcription Factor T-domain 1XBR   Hyperthermophile DNA 1AZP   Arc repressor 1PAR Other       ReI homology 1SVC   Stat protein 1BF5 Enzyme       Methyltransferase 6MHT   Endonuclease PvuII 3PVI   Endonuclease ecorV 1RVA   Endonuclease ecorI 1QPS   Endonuclease BamHI 3BAM   Enonuclease V 1VAS   Dnase I 2DNJ   DNA mismatch endonuclease 1CW0   DNA polymerase β 1BPY   DNA Polymerase I 2BDP   DNA Polymerase T7 1T7P,1CLQ   HIV Reverse Transcriptase 2HMI   Uracil DNA glycosylase 1SSP   3-Methyladenine DNA glycosylase 1BNK   Homing endonuclease 1A73, 1BP7   TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).

Publication Year: 2012

Reliable B cell epitope predictions: impacts of method development and improved benchmarking.

(2012) PLoS Comput Biol 8

PubMed: 23300419 | PubMedCentral: PMC3531324 | DOI: 10.1371/journal.pcbi.1002829

The PDB files were further processed into 2 different files: 1) only containing the chain interacting with the antibody as original defined in the DiscoTope dataset and 2) PDB files containing additio... al structural information on the biological relevant unit (as described in the publication associated with the structure) if available (obtainable for PDB entry: 1XIW, 1TZH, 1CZ8, 1BJ1, 1K4D, 1K4C, 1KYO, 1EZV, 1NCA, 1NMC, 1A14, 1NCB, 1NCC, 1NCD, 1OTS, 1AR1, 1NFD, 2HMI, 1EO8, 1QFU).

Publication Year: 2012

Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.

(2013) Nucleic Acids Res 41

PubMed: 23275546 | PubMedCentral: PMC3561941 | DOI: 10.1093/nar/gks1251

Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA     Poliovirus PV 1RA6 ( 3 ) 4... 1     Poliovirus (open) PV 3OL6 ( 9 ) 471     Poliovirus (closed) PV 3OL7 ( 9 ) 471     Coxsackie virus COXV 3DDK ( 11 ) 462     Human rhinovirus HRV 1XR6 ( 12 ) 460     Human rhinovirus HRV 1XR7 ( 12 ) 460     Foot and mouth disease virus FMDV 1U09 ( 2 ) 476 Caliciviridae, RdRp, +ssRNA     Norwalk virus NV 1SH0 ( 13 ) 510     Rabbit hemorrhagic disease virus RHDV 1KHV ( 14 ) 516     Rabbit hemorrhagic disease virus RHDV 1KHW ( 14 ) 516     Sapporo virus SAPV 2CKW ( 15 ) 515 Flaviviridae, RdRp, +ssRNA     Hepatitis C virus HCV 1NB4 ( 16 ) 570     Hepatitis C virus HCV 1NB7 ( 16 ) 570     Bovine viral diarrhea virus BVDV 1S48 ( 17 ) 609     West Nile (Kunjin) virus WNV 2HCS ( 18 ) 595     Dengue virus DENV 2J7U ( 19 ) 635 Cystoviridae, RdRp, dsRNA     Bacteriophage Phi6 PHI6 1HHS ( 20 ) 664     Bacteriophage Phi6 PHI6 1HI0 ( 20 ) 664 Reoviridae, RdRp, dsRNA     Reovirus lambda 3 REOV 1MUK ( 21 ) 1267     Reovirus lambda 3 REOV 1N35 ( 21 ) 1267     Rotavirus ROTAV 2R7X ( 22 ) 1095 Birnaviridae, RdRp, dsRNA     Infectious bursal disease, birnavirus IBDV 2PGG ( 5 ) 774     Infectious pancreatic necrosis IPNV 2YI8 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YI9 ( 23 ) 799     Infectious pancreatic necrosis IPNV 2YIA ( 23 ) 799 RdDp     HIV1 HIV1 1RT1 ( 24 ) 560     HIV1 (closed) HIV1 1RTD ( 25 ) 554     HIV1 (open) HIV1 2HMI ( 26 ) 558     Tribolium castaneum TERT 3DU6 ( 27 ) 596 DdRp     Bacteriophage T7 (closed) T7 RNAP 1S77 ( 28 ) 883     Bacteriophage T7 (closed) T7 RNAP 2AJQ ( 29 ) 704     Bacteriophage T7 (open) T7 RNAP 1MSW ( 30 ) 883     Bacteriophage N4 N4 3C2P ( 31 ) 1117 DdDp     Thermus aquaticus (open) TAQ 2KTQ ( 32 ) 538     Thermus aquaticus (closed) TAQ 3KTQ ( 32 ) 540     Thermus aquaticus (open) TAQ 4KTQ ( 32 ) 539     Bacteriophage T7 T7 DNAP 1T7P ( 33 ) 698 Queries of both open and closed structures were used to assess the impact of this feature on R2R correspondence.

Publication Year: 2013

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

DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.

(2014) PLoS One 9

PubMed: 24586799 | PubMedCentral: PMC3931789 | DOI: 10.1371/journal.pone.0089466

For 13 complexes no solution with i_rmsd <10 Å was found in the top 2000 predictions by knowledge-driven docking with DrugScore PPI /FRODOCK, four of which are classified as easy (PDB ... D’s: 1I4D, 1I9R, 1SBB, 2VIS), two as medium (1BGX, 1M10), and seven as difficult (1BKD, 1DE4, 1IBR, 1IRA, 1R8S, 1Y64, 2HMI) cases.

Four of these complexes are antigen-antibody complexes (PDB-ID’s: 1BGX, 1I9R, 2HMI, 2VIS); one of the complexes has already been discussed above regarding crystal packing effects (PDB-ID: 1I4D).

For five protein-protein complexes, no near-native solution could be found at all by DrugScore PPI /FRODOCK: Three of them are antigen-antibody complexes (see above; PDB-IDs: 1E6J, 1I9R, 2HMI), and two are other complexes (PDB-IDs: 1GLA, 1I4D).

Publication Year: 2014

An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24564934 | PubMedCentral: PMC3952246 | DOI: 10.1186/1472-6807-13-S1-S10

Enolase Superfamily (homogeneous): Enolases: 1e9i , 1iyx , 1pdy , 2pa6 , 2xsx , 2xsx Enolase Superfamily (homogeneous, redundant): Enolases: 1ebh , 1els , 1nel , 2al2 , 3enl , 7enl , 1te6 , 1ebg , 1on... Tyrosine Kinases (homogeneous): Small Gatekeeper residue: 1qcf , 1fgi , 1fpu , 1fvr , 1gjo , 1irk , 1k2p , 1m14 , 1m7n , 1qpc , 1r0p , 1t45 , 1u4d , 1yvj , 1ywn , 2src Tyrosine Kinases (homogeneous, redundant): Small Gatekeeper residue: 2hz4 , 2e2b , 2hyy , 2hz0 , 2hzn , 2hzi , 2xyn , 2hmi , 3kf4 , 3kfa , 3ms9 , 3mss Enolase Superfamily (heterogeneous): Enolases: 1e9i , 1ebh , 1iyx , 1pdy , 1te6 , 2pa6 , 2xsx , 3otr , Mandelate Racemase: 2ox4 , Muconate Lactonizing Enzyme: 2pgw , 2zad Tyrosine Kinases (heterogeneous): Small Gatekeeper residue: 2hz4 Large Gatekeeper residue: 1fvr , 1luf , 1rjb , 1sm2 , 1snu , 1snx Bolded structures were selected as templates.

Publication Year: 2013

Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.

(2013) Nat Struct Mol Biol 20

PubMed: 23314251 | PubMedCentral: PMC3973182 | DOI: 10.1038/nsmb.2485

One was co-crystallized with a monoclonal antibody bound to p51 (PDB: 2HMI) 38 , and the other with the PPT RNA/DNA hybrid (PDB: 1HYS) 30 .

Publication Year: 2013

Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition.

(2014) PeerJ 2

PubMed: 25071993 | PubMedCentral: PMC4103094 | DOI: 10.7717/peerj.470

10.7717/peerj.470/fig-2 Figure 2 Preferential binding mode of ligand 28 to HIV reverse transcriptase, as computed with AutoDock, with superposed DNA molecule taken from the DNA-bound HIV structure (PD... : 2HMI) ( Ding et al., 1998 ).

Application of this method to the catalytically active “open” conformation of HIV-1 reverse transcriptase (PDB: 2HMI) ( Ding et al., 1998 ) shows that inclusion of a coarse-grained representation of γ -rubromycin in the proposed binding site does not affect the protein flexibility: indeed, hardly any changes in vibrational modes are observed, as confirmed by the very high correlation coefficients between the normal modes of ligand-bound and empty reverse transcriptase, which always exceeding 0.9977.

Side-view (A) and “top”-view (B) of nucleic acid-bound reverse transcriptase (PDB: 2HMI) ( Ding et al., 1998 ).

Publication Year: 2014