Citations in PubMed

Primary Citation PubMed: 15565146 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I.

(2005) Nucleic Acids Res 33

PubMed: 16361267 | PubMedCentral: PMC1316110 | DOI: 10.1093/nar/gki1006

ATP-dependent DNA ligases To compare docking results and to identify compounds with specificity for LigA, well-characterized ATP ligases from two different sources, viral (T4) and human ATP-dependent ... igase I (PDB: 1X9N) were also chosen for docking studies.

Two structures each, namely Efa LigA (PDB: 1TAE) and Mtu LigA (PDB: 1ZAU), were used in screening for affinity for NAD + -dependent enzymes while T4 DNA ligase (a homology model) and Human DNA ligase I (PDB: 1X9N) were used for ATP-dependent enzymes.

Publication Year: 2005

Relative stabilities of conserved and non-conserved structures in the OB-fold superfamily.

(2009) Int J Mol Sci 10

PubMed: 19564956 | PubMedCentral: PMC2695284 | DOI: 10.3390/ijms10052412

Of the 95 domains classified as OB-fold motifs in SCOP, six structures (1CKM, 1HR0, 1J5E_L, 1J5E_Q, 1MIU, 1X9N) were discarded because of low resolution and/or errors, including two structures that ha... a knot in the main-chain (1X9N and 1CKM).

Publication Year: 2009

DNA mismatch repair in eukaryotes and bacteria.

(2010) J Nucleic Acids 2010

PubMed: 20725617 | PubMedCentral: PMC2915661 | DOI: 10.4061/2010/260512

PDB IDs of crystal structures in this figure are 2O8B (human MutS α ), 1H7S (human MutL α ), 1L1O (human RPA), 3IAY (human DNA polymerase δ ), 1X9N (human DNA ligase 1), 1E3M (... acterial MutS), 1B63 (bacterial MutL), 2AZO ( E. coli MutH), 2ISI (bacterial UvrD), 2ZXO (bacterial RecJ), 3C95 (bacterial ExoI), 2CWA (bacterial SSB), 2HQA (bacterial DNA polymerase III), and 2OWO (bacterial DNA ligase).

Publication Year: 2010

Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1.

(2010) PLoS Negl Trop Dis 4

PubMed: 20808768 | PubMedCentral: PMC2927429 | DOI: 10.1371/journal.pntd.0000803

A structural and sequence alignment of the superfamily members [18] reveals key sequence differences in relative positions between REL1 and human DNA ligase (PDB: 1X9N).

In human DNA ligase 1 (PDB 1X9N), the equivalent residues are M543-L544-A545-H546.

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

This flexible, multidomain ligase encompasses the duplex DNA with the adenylation domain binding to the nick; a binding mode also found in the human DNA ligase 1 bound to nicked DNA (pdb 1x9n ) [ 102 ... .

Publication Year: 2010

Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach.

(2011) 3 Biotech 1

PubMed: 22558535 | PubMedCentral: PMC3339591 | DOI: 10.1007/s13205-011-0006-8

2000 ), having PDB id 1x9n (A chain).

Modelling nsSNPs on protein structure and determining alterations in energy and RMSD The structure of the gene product LIG1 was acquired from PDB, having PDB id 1x9n (A chain).

end rs3730842 Intron −/3.6/ 3.6 T00601 NF-1 (-like proteins) + 19 48,672,996 48,673,009 rs75696040 Intron −/3.6/ 3.6 M00084 MZF1 – 19 48,673,165 48,673,177 rs74747924 Intron −/3.6/ 3.6 M00084 MZF1 – 19 48,673,165 48,673,177 rs7246696 Intron −/3.6/ 3.6 T03717 ZAP1 – 19 48,673,210 48,673,220 rs3730840 Intron −/2.7/ 2.7 M00720 CAC-binding protein – 19 48,673,455 48,673,463 rs3730838 Promoter 1.2/5.2/ 4.0 M00442 ABF + 19 48,673,851 48,673,866 rs752084 Promoter −/3.1/ 3.1 M00273 R + 19 48,673,926 48,673,944 rs3730836 Promoter −/2.3/ 2.3 MA0054 myb.Ph3 + 19 48,674,356 48,674,364 rs79501686 Promoter 0.1/1.5/1.4 MA0073 RREB1 – 19 48,674,851 48,674,870 a Description of Scores, Bef score of the TFBS in absence of SNP, Aft score of the TFBS in presence of SNP, Diff difference in Bef and Aft scores The scores in bold indicate substantial change in binding affinity of transcription factors in presence of SNP Mapping and analysis of mutants on protein structure Seven nsSNPs (rs11666150, rs55950593, rs34087182, rs3731003, rs117019444, rs3730947 and rs111507847) predicted to be deleterious by SIFT or PolyPhen server and present between the residue number 262 and 901 were mapped on the protein structure (PDB id: 1x9n, A chain) of gene product LIG1.

Publication Year: 2011

Structural insights into the role of domain flexibility in human DNA ligase IV.

(2012) Structure 20

PubMed: 22658747 | PubMedCentral: PMC3391681 | DOI: 10.1016/j.str.2012.04.012

In parallel, protein structures of LigIV homologs (human LigI [PDB code: 1X9N ]; Pascal et al., 2004 ), human LigIII (PDB code: 3L2P ; Cotner-Gohara et al., 2010 ), and three archeal D... A ligases (PDB codes 2HIV [ Pascal et al., 2006 ], 2CFM [ Nishida et al., 2006 ], and 3GDE [ Kim et al., 2009 ]) were downloaded from RSBC PDB ( Berman et al., 2000 ), and were structurally aligned using BATON (D.F. Burke, personal communication).

Figure 5 Comparison of the DNA-Binding Loop D1 of NTase-3 The structure of NTase-3 of LigIV (cyan) is shown together with that of LigI (I, pink; PDB code: 1X9N ) and LigIII (III, blue; PDB code: 3L2P ), and DNA (PDB code: 1X9N ).

To gain further insights into the role(s) of these residues, the structure of the entire NTase of LigIV was built using Modeller with the NTase-3 structure of LigIV and the experimentally defined domains from LigI (Protein Data Bank [PDB] code: 1X9N ), LigIII (PDB code: 3L2P ), and archeal DNA ligases (PDB codes: 2HIV , 2CFM , and 3GDE ) as templates ( Figure S5 B).

Publication Year: 2012

Saccharomyces cerevisiae DNA ligase IV supports imprecise end joining independently of its catalytic activity.

(2013) PLoS Genet 9

PubMed: 23825968 | PubMedCentral: PMC3694833 | DOI: 10.1371/journal.pgen.1003599

( C ) DNA ligase catalytic active site showing a structural alignment of hLig1 bound to a 5′-adenylated DNA nick (PDB 1X9N [5] , shaded more lightly) and adenylated Chlorella virus ligase boun... to a nick (PDB 2Q2T [22] , shaded more darkly).

Publication Year: 2013