Citations in PubMed

Primary Citation PubMed: 1557122 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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

DNA-binding residues and binding mode prediction with binding-mechanism concerned models.

(2009) BMC Genomics 10 Suppl 3

PubMed: 19958487 | PubMedCentral: PMC2788376 | DOI: 10.1186/1471-2164-10-S3-S23

Table 5 Dataset of 253 TF-DNA complexes for DNA-binding residues prediction 253 TF-DNA Complexes 1A02:F 1A02:J 1A0A:A 1A0A:B 1A6Y:A 1A6Y:B 1AKH:A 1AKH:B 1AM9:A 1AM9:B 1AM9:C 1AM9:D 1AN2:A 1AN4:A 1AN4:... 1APL:C 1APL:D 1AU7:A 1AU7:B 1B01:A 1B01:B 1B72:B 1B8I:B 1BDT:A 1BDT:B 1BDT:C 1BDT:D 1BDV:A 1BDV:B 1BDV:C 1BDV:D 1BY4:A 1BY4:B 1BY4:C 1BY4:D 1C0W:A 1C0W:B 1C0W:C 1C0W:D 1CF7:A 1CF7:B 1CGP:A 1CGP:B 1CMA:A 1CMA:B 1CQT:A 1D5Y:A 1D5Y:B 1D5Y:C 1D5Y:D 1D66:A 1D66:B 1DDN:A 1DDN:B 1DDN:C 1DDN:D 1DSZ:A 1DSZ:B 1DU0:A 1DU0:B 1EA4:A 1EA4:B 1EA4:D 1EA4:E 1EA4:F 1EA4:G 1EA4:H 1EA4:J 1EA4:K 1EA4:L 1F2I:G 1F2I:H 1F2I:I 1F2I:J 1F2I:K 1F2I:L 1F5T:A 1F5T:B 1F5T:C 1F5T:D 1FJL:A 1FJL:B 1FJL:C 1FOS:E 1FOS:F 1FOS:G 1FOS:H 1G2D:C 1G2D:F 1G2F:C 1G2F:F 1GDT:A 1GDT:B 1H88:A 1H88:B 1H89:A 1H89:B 1H8A:A 1H8A:B 1H9T:A 1H9T:B 1HCQ:A 1HCQ:B 1HDD:C 1HDD:D 1HF0:A 1HF0:B 1HJB:A 1HJB:B 1HJB:D 1HJB:E 1HLO:A 1HLO:B 1HW2:A 1HW2:B 1HWT:C 1HWT:D 1HWT:G 1HWT:H 1IO4:A 1IO4:B 1JGG:A 1JGG:B 1JNM:A 1JNM:B 1JT0:A 1JT0:B 1JT0:C 1JT0:D 1JWL:A 1JWL:B 1K61:A 1K61:B 1K61:C 1K61:D 1KB2:A 1KB2:B 1KB4:A 1KB4:B 1KB6:A 1KB6:B 1KU7:A 1L3L:A 1L3L:B 1L3L:C 1L3L:D 1LAT:A 1LAT:B 1LB2:A 1LE8:A 1LE8:B 1LLI:A 1LLI:B 1LLM:C 1LMB:3 1LMB:4 1MDY:A 1MDY:C 1MDY:D 1MEY:C 1MEY:F 1MJM:A 1MJM:B 1MJP:A 1MJP:B 1MNM:C 1MNM:D 1NKP:A 1NKP:B 1NKP:D 1NKP:E 1NLW:A 1NLW:B 1NLW:D 1NLW:E 1P47:A 1P47:B 1PAR:A 1PAR:B 1PAR:C 1PAR:D 1PER:L 1PER:R 1PUF:A 1PUF:B 1PYI:A 1PYI:B 1QP9:A 1QP9:B 1QP9:C 1QP9:D 1R0N:A 1RPE:L 1RPE:R 1TF6:A 1TF6:D 1TRO:A 1TRO:C 1TRO:E 1TRO:G 1TRR:A 1TRR:B 1TRR:D 1TRR:E 1TRR:G 1TRR:H 1TRR:J 1TRR:K 1YRN:A 1YRN:B 1YSA:C 1YSA:D 1ZME:C 1ZME:D 2DRP:A 2DRP:D 2HAP:C 2HAP:D 2HDD:A 2HDD:B 2NLL:A 2NLL:B 2OR1:L 2OR1:R 2PRT:A 2QL2:A 2QL2:B 2QL2:C 2QL2:D 2R5Y:A 2R5Y:B 3BPY:A 3CBB:A 3CBB:B 3CO6:C 3COQ:A 3COQ:B 3D0A:A 3D0A:B 3D0A:C 3D0A:D 3DFX:A 3DFX:B 3DZY:A 3DZY:D 3E00:A 3E00:D 3EXJ:A 3EXJ:B 3EXL:A 3HDD:A 3HDD:B 9ANT:A Defining the DNA-binding residue Previous research used various distance cut-offs from 3.5 Å to 6 Å to define DNA-binding residues between proteins and DNA [ 6 - 10 , 14 , 40 , 42 ].

Publication Year: 2009

Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network.

(2014) Nat Commun 5

PubMed: 25204769 | PubMedCentral: PMC4172970 | DOI: 10.1038/ncomms5868

Sequence comparison and fold recognition using Phyre2 indicated pdb entry 1D66 (Gal4-DNA complex) as the most suitable template 40 61 .

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4482085

In another type of dimerization of Zn(II)2Cys6 TF monomers, the co-crystal model of the S. cerevisiae Zn(II)2Cys6 factor Gal4 (PDB ID: 1D66) ( 60 ) shows that Lys20, Cys21 and Lys23 of each monomer ar... in contact with DNA backbone 5′-phosphate groups in the end bases C of the plus and minus motifs ( 61 ).

Publication Year: 2015