1SM1 Ribosome Antibiotic date Mar 08, 2004
title Complex Of The Large Ribosomal Subunit From Deinococcus Radi With Quinupristin And Dalfopristin
authors J.M.Harms, F.Schluenzen, P.Fucini, H.Bartels, A.Yonath
compound source
Molecule: 23s Ribosomal Rna
Chain
Engineered: Yes
Synthetic: Yes

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L36
Chain: 4

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: Quinupristin
Chain: 5
Synonym: Pristinamycin Ia, Rp 57669
Engineered: Yes

Synthetic: Yes
Organism_scientific: Streptomyces Graminofacien
Organism_taxid: 68212

Molecule: 5s Ribosomal Rna
Chain: 9
Engineered: Yes

Synthetic: Yes

Molecule: 50s Ribosomal Protein L2
Chain: A

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L3
Chain: B

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L9
Chain: F

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L11
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L16
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: P

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: S

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: General Stress Protein Ctc
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: W

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: X

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L31
Chain: Y

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
symmetry Space Group: I 2 2 2
R_factor 0.278 R_Free 0.348
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.500 406.000 693.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.42 Å
ligand 004, DBB, DOL, MHT, MHU, MHV, MHW enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


W


X


Y


Z


Primary referenceAlterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin., Harms JM, Schlunzen F, Fucini P, Bartels H, Yonath A, BMC Biol 2004 Apr 1;2(1):4. PMID:15059283
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1129 Kb) [Save to disk]
  • Biological Unit Coordinates (1sm1.pdb1.gz) 1120 Kb
  • LPC: Ligand-Protein Contacts for 1SM1
  • CSU: Contacts of Structural Units for 1SM1
  • Likely Quarternary Molecular Structure file(s) for 1SM1
  • Retrieve 1SM1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SM1 from S2C, [Save to disk]
  • View 1SM1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1SM1
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1SM1, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sm11_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1sm12_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1sm13_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1sm14_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1sm1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1sm1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1sm1c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1sm1d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1sm1e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1sm1f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1sm1g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1sm1h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1sm1i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1sm1j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1sm1k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1sm1l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1sm1m_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1sm1n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1sm1o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1sm1p_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1sm1q_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1sm1r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1sm1s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1sm1t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1sm1u_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1sm1w_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1sm1x_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1sm1y_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1sm1z_, region Z [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1sm1_W] [1sm1] [1sm1_X] [1sm1_1] [1sm1_A] [1sm1_Y] [1sm1_G] [1sm1_O] [1sm1_C] [1sm1_N] [1sm1_I] [1sm1_0] [1sm1_U] [1sm1_2] [1sm1_J] [1sm1_S] [1sm1_F] [1sm1_R] [1sm1_9] [1sm1_Q] [1sm1_Z] [1sm1_H] [1sm1_D] [1sm1_4] [1sm1_E] [1sm1_T] [1sm1_5] [1sm1_3] [1sm1_B] [1sm1_M] [1sm1_K] [1sm1_L] [1sm1_P]
  • SWISS-PROT database: [Q9RSS7] [Q9RXY1] [Q9RXJ2] [Q9RSK9] [Q9RXJ5] [Q9RSJ5] [Q9RSL2] [Q9RWB4] [Q9RSW7] [Q9RY64] [Q9RXJ7] [Q9RXK0] [Q9RXJ1] [Q9RX88] [Q9RY65] [Q9RXJ4] [Q9RXJ9] [Q9RSL0] [Q9RW44] [P49228] [Q9RSS4] [Q9RSH2] [Q9RSW6] [Q9RSK0] [Q9RXK2] [Q9RXK1] [Q9RXJ0] [Q9RSL3] [Q9RY49]
  • Domain organization of [RL11_DEIRA] [RL13_DEIRA] [RL14_DEIRA] [RL15_DEIRA] [RL16_DEIRA] [RL17_DEIRA] [RL18_DEIRA] [RL19_DEIRA] [RL20_DEIRA] [RL21_DEIRA] [RL22_DEIRA] [RL23_DEIRA] [RL24_DEIRA] [RL25_DEIRA] [RL27_DEIRA] [RL29_DEIRA] [RL2_DEIRA] [RL30_DEIRA] [RL31_DEIRA] [RL32_DEIRA] [RL33_DEIRA] [RL34_DEIRA] [RL35_DEIRA] [RL36_DEIRA] [RL3_DEIRA] [RL4_DEIRA] [RL5_DEIRA] [RL6_DEIRA] [RL9_DEIRA] by SWISSPFAM
  • Domains found in 1SM1: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 1SM1
  • Community annotation for 1SM1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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