Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 50S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400. DOI:10.2210/pdb2qba/pdb   NDB ID: RR0174

2QBA   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Split Entry The asymmetric unit for this structure is composed of multiple PDB entries: 2QB9   2QBA   2QBB   2QBC     Download All Files      Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Ribosome Structure Weight: 1359176.50 Molecule: 5S rRNA Polymer: 1 Type: rna Length: 120 Chains: A Organism Escherichia coli Molecule: 23S rRNA Polymer: 2 Type: rna Length: 2904 Chains: B Organism Escherichia coli Molecule: 50S ribosomal protein L11 Polymer: 3 Type: protein Length: 141 Chains: I Organism Escherichia coli Gene Names rplK relC b3983 JW3946 UniProtKB:   Protein Feature View | Search PDB | P0A7J7     Molecule: 50S ribosomal protein L2 Polymer: 4 Type: protein Length: 272 Chains: C Organism Escherichia coli Gene Names rplB b3317 JW3279 UniProtKB:   Protein Feature View | Search PDB | P60422     Molecule: 50S ribosomal protein L3 Polymer: 5 Type: protein Length: 209 Chains: D Organism Escherichia coli Gene Names rplC b3320 JW3282 UniProtKB:   Protein Feature View | Search PDB | P60438     Molecule: 50S ribosomal protein L14 Polymer: 6 Type: protein Length: 123 Chains: K Organism Escherichia coli Gene Names rplN b3310 JW3272 UniProtKB:   Protein Feature View | Search PDB | P0ADY3     Molecule: 50S ribosomal protein L19 Polymer: 7 Type: protein Length: 114 Chains: P Organism Escherichia coli Gene Names rplS b2606 JW2587 UniProtKB:   Protein Feature View | Search PDB | P0A7K6     Molecule: 50S ribosomal protein L4 Polymer: 8 Type: protein Length: 201 Chains: E Organism Escherichia coli Gene Names rplD eryA b3319 JW3281 UniProtKB:   Protein Feature View | Search PDB | P60723     Molecule: 50S ribosomal protein L30 Polymer: 9 Type: protein Length: 58 Chains: Y Organism Escherichia coli Gene Names rpmD b3302 JW3264 UniProtKB:   Protein Feature View | Search PDB | P0AG51     Molecule: 50S ribosomal protein L32 Polymer: 10 Type: protein Length: 56 Chains: 0 Organism Escherichia coli Gene Names rpmF b1089 JW1075 UniProtKB:   Protein Feature View | Search PDB | P0A7N4     Molecule: 50S ribosomal protein L36 Polymer: 11 Type: protein Length: 38 Chains: 4 Organism Escherichia coli Gene Names rpmJ b3299 JW3261 UniProtKB:   Protein Feature View | Search PDB | P0A7Q6     Molecule: 50S ribosomal protein L33 Polymer: 12 Type: protein Length: 54 Chains: 1 Organism Escherichia coli Gene Names rpmG b3636 JW3611 UniProtKB:   Protein Feature View | Search PDB | P0A7N9     Molecule: 50S ribosomal protein L35 Polymer: 13 Type: protein Length: 64 Chains: 3 Organism Escherichia coli Gene Names rpmI b1717 JW1707 UniProtKB:   Protein Feature View | Search PDB | P0A7Q1     Molecule: 50S ribosomal protein L25 Polymer: 14 Type: protein Length: 94 Chains: V Organism Escherichia coli Gene Names rplY b2185 JW2173 UniProtKB:   Protein Feature View | Search PDB | P68919     Molecule: 50S ribosomal protein L34 Polymer: 15 Type: protein Length: 46 Chains: 2 Organism Escherichia coli Gene Names rpmH rimA ssaF b3703 JW3680 UniProtKB:   Protein Feature View | Search PDB | P0A7P5     Molecule: 50S ribosomal protein L15 Polymer: 16 Type: protein Length: 144 Chains: L Organism Escherichia coli Gene Names rplO b3301 JW3263 UniProtKB:   Protein Feature View | Search PDB | P02413     Molecule: 50S ribosomal protein L16 Polymer: 17 Type: protein Length: 136 Chains: M Organism Escherichia coli Gene Names rplP b3313 JW3275 UniProtKB:   Protein Feature View | Search PDB | P0ADY7     Molecule: 50S ribosomal protein L29 Polymer: 18 Type: protein Length: 63 Chains: X Organism Escherichia coli Gene Names rpmC b3312 JW3274 UniProtKB:   Protein Feature View | Search PDB | P0A7M6     Molecule: 50S ribosomal protein L9 Polymer: 19 Type: protein Length: 149 Chains: H Organism Escherichia coli Gene Names rplI b4203 JW4161 UniProtKB:   Protein Feature View | Search PDB | P0A7R1     Molecule: 50S ribosomal protein L13 Polymer: 20 Type: protein Length: 142 Chains: J Organism Escherichia coli Gene Names rplM b3231 JW3200 UniProtKB:   Protein Feature View | Search PDB | P0AA10     Molecule: 50S ribosomal protein L17 Polymer: 21 Type: protein Length: 127 Chains: N Organism Escherichia coli Gene Names rplQ b3294 JW3256 UniProtKB:   Protein Feature View | Search PDB | P0AG44     Molecule: 50S ribosomal protein L18 Polymer: 22 Type: protein Length: 117 Chains: O Organism Escherichia coli Gene Names rplR b3304 JW3266 UniProtKB:   Protein Feature View | Search PDB | P0C018     Molecule: 50S ribosomal protein L20 Polymer: 23 Type: protein Length: 117 Chains: Q Organism Escherichia coli Gene Names rplT pdzA b1716 JW1706 UniProtKB:   Protein Feature View | Search PDB | P0A7L3     Molecule: 50S ribosomal protein L22 Polymer: 24 Type: protein Length: 110 Chains: S Organism Escherichia coli Gene Names rplV eryB b3315 JW3277 UniProtKB:   Protein Feature View | Search PDB | P61175     Molecule: 50S ribosomal protein L24 Polymer: 25 Type: protein Length: 103 Chains: U Organism Escherichia coli Gene Names rplX b3309 JW3271 UniProtKB:   Protein Feature View | Search PDB | P60624     Molecule: 50S ribosomal protein L5 Polymer: 26 Type: protein Length: 178 Chains: F Organism Escherichia coli Gene Names rplE b3308 JW3270 UniProtKB:   Protein Feature View | Search PDB | P62399     Molecule: 50S ribosomal protein L6 Polymer: 27 Type: protein Length: 176 Chains: G Organism Escherichia coli Gene Names rplF b3305 JW3267 UniProtKB:   Protein Feature View | Search PDB | P0AG55     Molecule: 50S ribosomal protein L21 Polymer: 28 Type: protein Length: 103 Chains: R Organism Escherichia coli Gene Names rplU b3186 JW3153 UniProtKB:   Protein Feature View | Search PDB | P0AG48     Molecule: 50S ribosomal protein L23 Polymer: 29 Type: protein Length: 100 Chains: T Organism Escherichia coli Gene Names rplW b3318 JW3280 UniProtKB:   Protein Feature View | Search PDB | P0ADZ0     Molecule: 50S ribosomal protein L28 Polymer: 30 Type: protein Length: 78 Chains: Z Organism Escherichia coli Gene Names rpmB b3637 JW3612 UniProtKB:   Protein Feature View | Search PDB | P0A7M2     Molecule: 50S ribosomal protein L27 Polymer: 31 Type: protein Length: 84 Chains: W Organism Escherichia coli Gene Names rpmA b3185 JW3152 UniProtKB:   Protein Feature View | Search PDB | P0A7L8         Source Hide Polymer: 1 Scientific Name: Escherichia coli   Taxonomy     Polymer: 2 Scientific Name: Escherichia coli   Taxonomy     Polymer: 3 Scientific Name: Escherichia coli   Taxonomy     Polymer: 4 Scientific Name: Escherichia coli   Taxonomy     Polymer: 5 Scientific Name: Escherichia coli   Taxonomy     Polymer: 6 Scientific Name: Escherichia coli   Taxonomy     Polymer: 7 Scientific Name: Escherichia coli   Taxonomy     Polymer: 8 Scientific Name: Escherichia coli   Taxonomy     Polymer: 9 Scientific Name: Escherichia coli   Taxonomy     Polymer: 10 Scientific Name: Escherichia coli   Taxonomy     Polymer: 11 Scientific Name: Escherichia coli   Taxonomy     Polymer: 12 Scientific Name: Escherichia coli   Taxonomy     Polymer: 13 Scientific Name: Escherichia coli   Taxonomy     Polymer: 14 Scientific Name: Escherichia coli   Taxonomy     Polymer: 15 Scientific Name: Escherichia coli   Taxonomy     Polymer: 16 Scientific Name: Escherichia coli   Taxonomy     Polymer: 17 Scientific Name: Escherichia coli   Taxonomy     Polymer: 18 Scientific Name: Escherichia coli   Taxonomy     Polymer: 19 Scientific Name: Escherichia coli   Taxonomy     Polymer: 20 Scientific Name: Escherichia coli   Taxonomy     Polymer: 21 Scientific Name: Escherichia coli   Taxonomy     Polymer: 22 Scientific Name: Escherichia coli   Taxonomy     Polymer: 23 Scientific Name: Escherichia coli   Taxonomy     Polymer: 24 Scientific Name: Escherichia coli   Taxonomy     Polymer: 25 Scientific Name: Escherichia coli   Taxonomy     Polymer: 26 Scientific Name: Escherichia coli   Taxonomy     Polymer: 27 Scientific Name: Escherichia coli   Taxonomy     Polymer: 28 Scientific Name: Escherichia coli   Taxonomy     Polymer: 29 Scientific Name: Escherichia coli   Taxonomy     Polymer: 30 Scientific Name: Escherichia coli   Taxonomy     Polymer: 31 Scientific Name: Escherichia coli   Taxonomy         Related PDB Entries Hide Identifier Details 2QB9  30s subunit of 70s ribosome one  2QBB  30s subunit of 70s ribosome two  2QBC  50s subunit of 70s ribosome two      Ligand Chemical Component Hide Identifier Formula Name Interactions LLL Search  Download  C19 H39 N5 O7 (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO- 3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO- 2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)- 5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN- 3,5-DIOL   Ligand Explorer MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer ZN Search  Download  Zn ZINC ION   Ligand Explorer     External Domain Annotations Hide SCOP Classification v1.75: 32 Domains - data from SCOP   CATH Classification v3.4.0: 15 Domains - data from CATH   Pfam Classification: 34 Domains - data from Pfam   GO Terms: 217 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: RR0174     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Composite of PDB entries (2QB9 and 2QBA)         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Borovinskaya, M.A.,  Pai, R.D.,  Zhang, W.,  Schuwirth, B.-S.,  Holton, J.M.,  Hirokawa, G.,  Kaji, H.,  Kaji, A.,  Cate, J.H.D. Deposition:   2007-06-16 Release:   2007-09-25 Last Modified (REVDAT):   2009-02-24     Revision History    Hide Mouse over text for details 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors Resolution[Å]:   3.54 R-Value: 0.281 (work) R-Free: 0.320 Space Group: P 21 21 21 Unit Cell:   Length [Å] Angles [°] a = 208.85 α = 90.00  b = 379.20 β = 90.00  c = 739.28 γ = 90.00      Molecule of the Month Hide Ribosome Transfer-Messenger RNA