Citations in PubMed

Primary Citation PubMed: 10535734 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 7

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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Insights into protein-DNA interactions through structure network analysis.

(2008) PLoS Comput Biol 4

PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170

Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).

Publication Year: 2008


Modeling of loops in proteins: a multi-method approach.

(2010) BMC Struct Biol 10

PubMed: 20149252 | PubMedCentral: PMC2837870 | DOI: 10.1186/1472-6807-10-5

loop length PDB codes and loop ranges 4 7rsa 47-50, 4gcr 116-119, 2tgi 72-75, 2exo 161-164, 1xif 82-85, 1tml 42-45, 1tib 46-49, 1thw 194-197, 1rcf 111-114, 1ppn 42-45, 1plc 74-77, 1pbe 117-120, 1nfp 3... -40, 1frd 59-62, 1cbs 21-24, 1ads 99-102, 1aaj 82-85 5 7rsa 75-79, 2hbg 37-41, 2cmd 188-192, 1vcc 63-67, 1tml 147-151, 1tca 157-161, 1sbp 181-185, 1prn 187-191, 1noa 88-92, 1nfp 95-99, 1nar 56-60, 1kuh 37-41, 1hbq 158-162, 1hbg 19-23, 1frd 83-87, 153l 131-135 6 5p21 104-109, 3pte 256-261, 3pte 131-136, 2ayh 81-86, 1tca 94-99, 1tca 38-43, 1rge 73-78, 1noa 25-30, 1mrp 233-238, 1gca 100-105, 1ede 180-185, 1cbs 66-71, 1brt 253-258, 1brt 174-179, 1ads 150-155, 1ads 149-154 7 5p21 83-89, 2pth 95-101, 1tml 20-26, 1tca 132-138, 1php 135-141, 1mbd 17-23, 1lif 64-70, 1iab 142-148, 1hbg 46-52, 1gca 196-202, 1edg 309-315, 1dad 116-122, 1brt 226-232, 1bkf 64-70, 1ads 186-192 8 2ayh 194-201, 1tml 187-194, 1thw 18-25, 1prn 150-157, 1nwp 84-91, 1nls 97-104, 1nar 192-199, 1hbq 31-38, 1arb 136-143, 1alc 34-41, 1ads 274-281 9 3pte 107-115, 2ayh 169-177, 1xnb 133-141, 1xnb 116-124, 1php 91-99, 1nls 131-139, 1ede 257-265, 1arb 168-176, 1aac 58-66 10 7rsa 87-96, 7rsa 33-42, 7rsa 110-119, 2cmd 57-66, 1whi 47-56, 1tca 23-32, 1scs 65-74, 1ppn 190-199, 1plc 42-51, 1mrj 173-182, 1ixh 84-93, 1gvp 49-58, 1fkf 63-72, 1arb 41-50, 1amp 181-190, 1ads 171-180, 1ads 170-179, 135l 18-27 11 3pte 91-101, 2pth 8-18, 1rcf 122-132, 1ixh 120-130, 1dad 42-52, 153l 154-164 12 2ayh 21-32, 1ixh 160-171, 1bkf 9-20, 1arb 74-85, 153l 98-109 16 1tml 73-88, 1tml 219-234, 1tca 184-199, 1rge 37-52, 1prn 106-121, 1nar 10-25, 1iab 136-151, 1frd 33-48, 1edg 233-248, 1edg 167-182, 1brt 57-72, 1amp 98-113, 1ads 210-225 18 1tml 73-90, 1tml 219-236, 1tca 184-201, 1prn 106-123, 1nar 10-27, 1iab 136-153, 1byt 807-824, 1byt 700-717, 1byt 359-376, 1byt 230-247, 1bst 57-74, 1bst 129-146, 1b57 209-226, 1awj 2-19, 1amp 98-115, 1ahj 101-118, 1ads 210-227, 1acc 36-53, 1acc 183-200 20 1br4 390-409, 1br4 349-368, 1br4 291-310, 1br2 246-265, 1azx 362-381 22 1tml 219-240, 1prn 106-127, 1nar 10-31, 1kk7 291-312, 1jez 117-138, 1itk 179-200, 1itk 157-178, 1e04 351-372, 1clq 380-401, 1br4 71-92, 1br4 256-277, 1b3k 322-343, 1aoa 182-203 23 1nfb 253-275, 1lzj 2-24, 1izl 21-43, 1i50 46-68, 1dzg 367-389 24 1uoz 224-247, 1mnd 277-300, 1miu 93-116, 1i19 415-438, 1hfb 86-109 25 2hs0 319-343, 2gah 437-461, 2fqf 293-317, 2e4y 311-335, 1zba 16-40, 1tml 219-243, 1qme 127-151, 1prn 106-130, 1kmh 117-141, 1eah 247-271, 1dms 596-620, 1dhx 376-400, 1dhx 11-35 Using MODELLER, we generated 500 examples of individual loop regions, which were subsequently ranked by the DOPE statistical potential [ 22 ].

Publication Year: 2010


Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.

(2010) Virol J 7

PubMed: 21129204 | PubMedCentral: PMC3012046 | DOI: 10.1186/1743-422X-7-359

T4 and Related Phage T7 Phage E. coli Eukaryotes Replicative DNA polymerase gp43 polymerase (pdb 1ig9 , 1clq , 1noy , 1ih7 ) Gene 5 Polymerase (pdb 1t7p , 1skr , 1t8e , 1x9m ) Pol III (α... 5;θ) (pdb 2hnh , 1ido ) Pol δ (subunits p125, p50, p66, p12) (pdb 3e0j ) Sliding clamp gp45 protein (pdb 1czd , 1b8h ) E. coli Thioredoxin (pdb 1t7p , 1skr ) β (pdb 2pol ) PCNA (pdb 1plr , 1axc , 1ul1 ) Clamp loader gp44/62 protein γ complex (γδδ'ψχ) (pdb 1jr3 , 1jqj , 3glf ) RF-C (subunits p140, p40, p38, p37, p36) (pdb 1sxj ) ssDNA binding protein gp32 protein (pdb 1gpc ) Gene 2.5 protein (pdb 1je5 ) SSB (pdb 1qvc ) RP-A (subunits p14, p32, p70) (pdb 1fgu , 2b29 , 1jmc , 1l1o , 2pi2 ) Replicative helicase gp41 helicase Gene 4 helicase (pdb 1e0j , 1e0k , 1q57 ) DnaB (pdb 1b79 , 2r6a ) MCM (pdb 3f9v , 1ltl ) helicase assembly protein gp59 protein (pdb 1c1k ) DnaC, PriA (pdb 3ec2 ) primase gp61 primase Gene 4 primase (pdb 1nui , 1q57 ) DnaG (pdb 1dd9 , 3b39 , 2r6c ) Pol α/primase (pdb 3flo ) 5' to 3' Exonuclease RNase H (pdb 1tfr , 2ihn ) Pol I N-domain FEN-1, RNase H1 (pdb 1ul1 , 2qk9 ) DNA ligase 1 T4 ligase (gp30) T7 ligase (pdb 1a0i ) DNA ligase (pdb 2owo ) DNA ligase I Figure 2 The molecular models, rendered to scale, of a DNA replication fork .

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


Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil.

(2013) Nucleic Acids Res 41

PubMed: 23303790 | PubMedCentral: PMC3575838 | DOI: 10.1093/nar/gks1364

Both structures are taken from editing complexes: Tgo -Pol (PDB ID, 2xhb) ( 8 ) and RB69-Pol (PDB ID 1clq) ( 12 ).

Publication Year: 2013


Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.

(2013) Nucleic Acids Res 41

PubMed: 23921641 | PubMedCentral: PMC3799440 | DOI: 10.1093/nar/gkt674

( A ) Superposition of the structure of wt RB69pol closed ternary complex (PDB: 3NCI, shown in blue) with the structure of the binary complex in an editing mode (PDB: 1CLQ, shown in gray).

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4018061

Scheme 1 Figure 8 (A) Superposition of the structure of the wt RB69pol closed ternary complex [Protein Data Bank (PDB) entry 3NCI] with the structure of the binary complex in an editing mode (PDB entr... 1CLQ).

Publication Year: 2014