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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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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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A model for the study of ligand binding to the ribosomal RNA helix h44.

(2010) Nucleic Acids Res 38

PubMed: 20215440 | PubMedCentral: PMC2910043 | DOI: 10.1093/nar/gkq159

Stereo view of a superposition of the hygromycin B binding site in HX RNA (white backbone) and the corresponding region in the crystal structures of the ribosomal 30S subunit, free (orange, PDB 1J5E; ... MSD = 1.2 Å) ( 25 ) and in complex with the aminoglycoside ligand (green, PDB 1HNZ; RMSD = 1.1 Å) ( 7 ).

RMSD values were calculated for superposition of residues C1403–C1409 and G1494–U1498; RMSD of 1J5E versus 1HNZ=0.4 Å.

Publication Year: 2010


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


Measuring the shapes of macromolecules - and why it matters.

(2013) Comput Struct Biotechnol J 8

PubMed: 24688748 | PubMedCentral: PMC3962087 | DOI: 10.5936/csbj.201309001

We use the structure of the complex hygromycin B - 30S as a reference (PDB code 1HNZ).

(A) The rRNA component of the 30S subunit of the ribosome of Thermus thermophilus (PDB code 1HNZ).

Publication Year: 2013