Citations in PubMed

Primary Citation PubMed: 11296217 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 3

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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Structural signatures of antibiotic binding sites on the ribosome.

(2010) Nucleic Acids Res 38

PubMed: 20494981 | PubMedCentral: PMC2952860 | DOI: 10.1093/nar/gkq411

Crystallographic structures of T. thermophilus (T.t) and E.coli (E.c) small subunit, and H. marismortui (H.m) and D. radiodurans (D.r) large subunit complexed to antibiotics Index Subunit Antibiotics ... W (Da) Organism PDB Identifier Resolution Refs 1 30S Hygromycin B 527.52 T.t 1HNZ HYG 3.3 Å ( 53 ) 2 30S Pactamycin 558.62 T.t 1HNX PCY 3.4 Å ( 53 ) 3 30S Tetracycline 444.44 T.t 1HNW TAC 1001 3.4 Å ( 53 ) 4 30S Tetracycline 444.44 T.t 1HNW TAC 1002 3.4 Å ( 53 ) 5 30S Tetracycline 444.44 T.t 1I97 TAC 2001 4.5 Å ( 7 ) 6 30S Tetracycline 444.44 T.t 1I97 TAC 2003 4.5 Å ( 7 ) 7 30S Tetracycline 444.44 T.t 1I97 TAC 2004 4.5 Å ( 7 ) 8 30S Tetracycline 444.44 T.t 1I97 TAC 2005 4.5 Å ( 7 ) 9 30S Tetracycline 444.44 T.t 1I97 TAC 2006 4.5 Å ( 7 ) 10 30S Edeine 781.9 T.t 1I95 EDE 4.5 Å ( 7 ) 11 30S Spectinomycin 332.35 T.t 1FJG SCM 3 Å ( 54 ) 12 30S Streptomycin 581.57 T.t 1FJG SRY 3 Å ( 54 ) 13 30S Paromomycinaromomycin 615.63 T.t 1FJG PAR 3 Å ( 54 ) 14 30S Kasugamycin 379.36 T.t 2HHH KSG 1523 3.35 Å ( 57 ) 15 30S Hygromycin B 527.52 E.c 3DF1 HYG 3.5 Å ( 58 ) 16 30S Spectinomycin 332.35 E.c 2QOU SCM 3.93 Å ( 59 ) 17 30S Kasugamycin 379.36 E.c 1VS5 KSG 3.5 Å ( 60 ) 18 30S Gentamicin 449.54 E.c 2QB9 LLL 2356 3.54 Å ( 10 ) 19 30S Gentamicin 449.54 E.c 2QB9 LLL 2357 3.54 Å ( 10 ) 20 30S Gentamicin 449.54 E.c 2QB9 LLL 2357 3.54 Å ( 10 ) 21 30S Neomycin 614.64 E.c 2QAL NMY 3.21 Å ( 10 ) 22 50S Erythromycin 733.93 H.m 1YI2 ERY 2.65 Å ( 56 ) 23 50S Azithromycin 748.99 H.m 1YHQ ZIT 2.4 Å ( 56 ) 24 50S Telithromycin 812.01 H.m 1YIJ TEL 3.4 Å ( 56 ) 25 50S Quinupristin 1022.22 H.m 1YJW SYB 2.9 Å ( 56 ) 26 50S Virginiamycin S 823.89 H.m 1YIT VRS 2.8 Å ( 56 ) 27 50S Virginiamycin M 525.59 H.m 1YIT VIR 2.8 Å ( 56 ) 28 50S Clindamycin 424.98 H.m 1YJN CLY 3 Å ( 56 ) 29 50S Carbomycin 841.98 H.m 1K8A CAI 3 Å ( 35 ) 30 50S Spiramycin 843.05 H.m 1KD1 SPR 3 Å ( 35 ) 31 50S Tylosin 916.1 H.m 1K9M TYK 3 Å ( 35 ) 32 50S Sparsomycin 361.44 H.m 1M90 SPS 2.8 Å ( 55 ) 33 50S Chloramphenicol 323.13 H.m 1NJI CLM 2.55 Å ( 3 ) 34 50S Anisomycin 265.31 H.m 1K73 ANM 3.01 Å ( 3 ) 35 50S Blasticidin S 422.44 H.m 1KC8 BLS 9001 3.01 Å ( 3 ) 36 50S Blasticidin S 422.44 H.m 1KC8 BLS 9002 3.01 Å ( 3 ) 37 50S Homoharringtonine 545.62 H.m 3G6E HMT 2.7 Å ( 61 ) 38 50S Bruceantin 548.58 H.m 3G71 WIN 3.85 Å ( 61 ) 39 50S Tiamulin 493.74 H.m 3G4S MUL 3.2 Å ( 61 ) 40 50S Oxazolidinone 513.52 H.m 3CXC SLD 3 Å ( 62 ) 41 50S Girodazole 190.63 H.m 2OTL GIR 2.7 Å ( 12 ) 42 50S 13-deoxytedanolide 594.73 H.m 2OTJ 13T 2.9 Å ( 12 ) 43 50S Erythromycin 733.93 D.r 1JZY ERY 3.5 Å ( 63 ) 44 50S Clindamycin 424.98 D.r 1JZX CLY 3.1 Å ( 63 ) 45 50S Clarithromycin 747.95 D.r 1J5A CTY 3.5 Å ( 63 ) 46 50S Roxithromycin 837.05 D.r 1JZZ ROX 3.8 Å ( 63 ) 47 50S Chloramphenicol 323.13 D.r 1K01 CLM 3.5 Å ( 63 ) 48 50S Azithromycin 748.99 D.r 1NWY ZIT 1 3.3 Å ( 64 ) 49 50S Azithromycin 748.99 D.r 1NWY ZIT 2 3.3 Å ( 64 ) 50 50S Cethromycin 765.93 D.r 1NWX 773 3.5 Å ( 64 ) 51 50S Telithromycin 812.01 D.r 1P9X TEL 3.4 Å ( 65 ) 52 50S Quinupristin 1022.22 D.r 1SM1 SYB 3.42 Å ( 66 ) 53 50S Dalfopristin 690.85 D.r 1SM1 DOL 3.42 Å ( 66 ) 54 50S Sparsomycin 361.44 D.r 1NJN SPS 3.7 Å ( 67 ) 55 50S Troleandomycin 813.97 D.r 1OND TAO 3.4 Å ( 68 ) 56 50S Tiamulin 493.74 D.r 1XBP MUL 3.5 Å ( 69 ) 57 50S Thiostrepton 1664.89 D.r 3CF5 TXX 3.3 Å ( 21 ) 58 50S Oxazolidinone 337.35 D.r 3DLL ZLD 3.5 Å ( 70 ) 59 50S SB-571519 498.57 D.r 2OGM G19 3.5 Å ( 45 ) 60 50S SB-280080 477.70 D.r 2OGN G80 3.56 Å ( 45 ) 61 50S SB-275833 517.76 D.r 2OGO G34 3.66 Å ( 45 ) 62 50S Rapamycin 914.17 D.r 1Z58 RAP 3.8 Å ( 13 ) 63 50S Josamycin 828.00 D.r 2O44 JOS 3.3 Å ( 71 ) 64 50S RU-69874 972.22 D.r 2O45 RU6 3.6 Å ( 71 ) 65 50S Erythromycylamine 734.96 D.r 2O43 ERN 3.6 Å ( 71 ) Extracting putative pockets in the ribosome The program ‘solvent’ from the 3V package ( http://geometry.molmovdb.org/3v/ ) was applied to identify putative pockets in the ribosome ( 22 ).

Publication Year: 2010


RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

(2010) Nucleic Acids Res 38

PubMed: 20696653 | PubMedCentral: PMC2952876 | DOI: 10.1093/nar/gkq672

To demonstrate this, we selected three PDB entries with different resolutions for the same 16S rRNA structure from Thermus thermophilus (PDBid: 2VQE, 1J5E and 1I95), and used RNAMotifScan to identify ... he five motifs in them.

bp #KT #CL #SR #RK #EL 2VQE 2.50 Å 1522 766 433 333 3 0 2 0 6 1J5E 3.05 Å 1522 761 434 327 2 0 2 0 6 1I95 4.50 Å 1514 699 422 277 1 0 0 0 3 The columns in the tables represent PDB codes of the RNA structures, the resolution, the length, the number of base pairs (bp) annotated by MC-Annotate, the number of annotated canonical base pairs (Can.

Publication Year: 2010


A structural basis for streptomycin-induced misreading of the genetic code.

(2013) Nat Commun 4

PubMed: 23322043 | PubMedCentral: PMC3552334 | DOI: 10.1038/ncomms2346

A similar disengaged tetraloop conformation was modeled for PDB entry 1N34 13 and entries 1I95, 1I96, and 1I97 34 .

Publication Year: 2013