Citations in PubMed

Primary Citation PubMed: 10385126 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

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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Variation in structural location and amino acid conservation of functional sites in protein domain families.

(2005) BMC Bioinformatics 6

PubMed: 16122386 | PubMedCentral: PMC1215474 | DOI: 10.1186/1471-2105-6-210

In contrast, a phenylalanine establishes the contact in figure 3b (pdb id: 1ckt [ 28 ]) and the serine residue corresponding to the structure shown in 3a is pointing away from the DNA helix.

Publication Year: 2005


Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.

(2008) Nucleic Acids Res 36

PubMed: 18515834 | PubMedCentral: PMC2475640 | DOI: 10.1093/nar/gkn353

Left, HMG box A from mammalian HMGB1 ( 37 , 38 , 41 ), PDB code 1CKT, which is highly similar to the corresponding box from HMGB2.

Publication Year: 2008


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


Structural basis for the sequence-dependent effects of platinum-DNA adducts.

(2009) Nucleic Acids Res 37

PubMed: 19255091 | PubMedCentral: PMC2677858 | DOI: 10.1093/nar/gkp029

For the simulations of HMGB1a-Pt–DNA complex, we used the crystal structure of rat HMGB1a bound to CP-DNA in the T GG A sequence context as the starting structure for the CP-T GG A simulations... [PDB ID 1ckt ( 21 )].

Publication Year: 2009


Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A.

(2009) Nucleic Acids Res 37

PubMed: 19304746 | PubMedCentral: PMC2691818 | DOI: 10.1093/nar/gkp157

Structural comparison of selected HMG boxes PDB Protein RMSD (Å) Method 2HDZ UBF box 5 1.35 X-Ray 1J3C HMGB2 box B 1.40 NMR 1QRV HMGD/DNA 1.49 X-Ray 2LEF LEF1/DNA 1.50 NMR 1CKT HMGB1 box A/DNA... 1.87 X-Ray 1J3X HMGB2 box A 2.04 NMR 1HMF HMGB1 box B 2.23 NMR 2YUL SOX17 2.28 NMR 2YQI HMGB3 box B 2.33 NMR 2EZQ HMGB3 box A 2.36 NMR 1V63 UBF box 6 2.38 NMR 1AAB HMGB1 box A 2.53 NMR 1GTO SOX2/DNA 2.93 X-Ray 1V64 UBF box 3 3.10 NMR 1K99 UBF box 1 3.13 NMR 1HRY SRY/DNA 3.73 NMR 1WGF UBF box 4 5.42 NMR Despite the differences in the tertiary structural features of box B of h-mtTFA compared to other HMG boxes, the surface electrostatic features of the HMG boxes are similar.

( A ) Structural superposition of box B of h-mtTFA (3fgh; red) overlaid with HMGD (1qrv; yellow), UBF box 5 (2hdz; green), LEF1 (2lef; purple), HMGB1 box A (1ckt; cyan) and Sox2 (1gt0; black).

Overall RMSD values were calculated between each amino acid of the structures of HMGD [PDB ID 1qrv ( 36 )], SOX2 HMG box A (PDB ID 1gt0, Remenyi, A., Scholer, H.R., Wilmanns, M. unpublished), HMGB1 box A [PDB ID 1ckt ( 37 )], LEF1 [PDB ID 2lef ( 38 )] and UBF5 [PDB ID 2hdz; Rong, H., Teng, M.K., and Niu, L., unpublished data)] and the X-ray crystal structure of h-mtTFA box B using the program COOT ( 33 ).

Publication Year: 2009


The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA.

(2011) Nat Struct Mol Biol 18

PubMed: 22037171 | PubMedCentral: PMC3210390 | DOI: 10.1038/nsmb.2159

Structures correspond to the following accession numbers, and RMSD values, relative to HMG-box A of Tfam, are provided in parentheses: HMG-box B of Tfam without DNA, 3fgh 19 (0.974); Hmgb1 box A, 1ckt... 27 (1.101); Lef1, 2lef 28 (1.162); Sox2, 1gt0 29 (1.152); Hmgd, 1qrv 30 (1.127).

Publication Year: 2011


A nuclear factor of high mobility group box protein in Toxoplasma gondii.

(2014) PLoS One 9

PubMed: 25369210 | PubMedCentral: PMC4219823 | DOI: 10.1371/journal.pone.0111993

TgHMGB1a is a typical one HMG box protein and concentrated in nuclear in intracellular tachyzoites but translocated into cytoplasm while it's in extracellular The ternary structure of full length TgHM... B1a ( Figure 2 A ) was modeled using the structure template of 1ckt A chain.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4373776

Following PDB structures were used: SRY—1j46 [ 36 ], HMGB1a-1ckt [ 41 ], MAEL HMG—2cto [ 45 ].

Determined structures of candidate HMG-box proteins (SRY: 1j46—sequence specific binding; HMGB1a: 1ckt—structure specific binding; MAEL: 2cto—unknown binding) were visualized and structures aligned in PyMOL.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4498601

This DNA and the full protein coordinates of HMGB1 box A (Pro8–Tyr77 in Fig. 1 ▸ ; Ohndorf et al. , 1999 ▸ ; PDB entry 1ckt ) were used as a search model for molecular replacem... nt.

Superimposition of box A from this structure (cyan) with ( a ) box A from cisplatin-modified DNA (PDB entry 1ckt ; gray; Ohndorf et al. , 1999 ▸ ), ( b ) box A from the solution structure of the oxidized form (PDB entry 2rtu ; gray; Wang et al. , 2013 ▸ ) and ( c ) the C22S mutant box A free reduced form (PDB entry 1aab ; gray; Hardman et al. , 1995 ▸ ).

The roll and twist angles for box A in this structure were obtained with 3 DNA , and those for PDB entries 1ckt (box A, cisplatin; Ohndorf et al. , 1999 ▸ ), 2gzk (box B; Stott et al. , 2006 ▸ ), 1qrv (HMGD; Murphy et al. , 1999 ▸ ), 1j5n (NHP6A; Masse et al. , 2002 ▸ ) and 3tmm (TFAM; Ngo et al. , 2011 ▸ ) were taken from the Nucleic Acids Data Bank (NDB; see also Supplementary Table S2).

Publication Year: 2015