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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.
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).
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).
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.
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 .
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 ).
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