1K9M Ribosome date Oct 29, 2001
title Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal Subunit Of Haloarcula Marismortui
authors J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Rrna
Chain: A
 Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Rrna
Chain: B
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L2
Chain: C
Synonym: 50s Ribosomal Protein L2p, Hmal2, Hl4
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L3
Chain: D
Synonym: 50s Ribosomal Protein L3p, Hmal3, Hl1
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L4
Chain: E
Synonym: 50s Ribosomal Protein L4e, Hmal4, Hl6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L5
Chain: F
Synonym: 50s Ribosomal Protein L5p, Hmal5, Hl13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L6
Chain: G
Synonym: 50s Ribosomal Protein L6p, Hmal6, Hl10
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L7ae
Chain: H
Synonym: 50s Ribosomal Protein Hs6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10
Chain: I
Synonym: 50s Ribosomal Protein P0, Hmal10, L10e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10e
Chain: J
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L13
Chain: K
Synonym: 50s Ribosomal Protein L13p, Hmal13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L14
Chain: L
Synonym: 50s Ribosomal Protein L14p, Hmal14, Hl27
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15
Chain: M
Synonym: 50s Ribosomal Protein L15p, Hmal15, Hl9
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15e
Chain: N
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18
Chain: O
Synonym: 50s Ribosomal Protein L18p, Hmal18, Hl12
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18e
Chain: P
Synonym: 50s Ribosomal Protein L18e, Hl29, L19
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L19e
Chain: Q
Synonym: 50s Ribosomal Protein L19e, Hmal19, Hl24
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L21e
Chain: R
Synonym: 50s Ribosomal Protein L21e, Hl31
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L22
Chain: S
Synonym: 50s Ribosomal Protein L22p, Hmal22, Hl23
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L23
Chain: T
Synonym: 50s Ribosomal Protein L23p, Hmal23, Hl25, L21
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24
Chain: U
Synonym: 50s Ribosomal Protein L24p, Hmal24, Hl16, Hl15
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24e
Chain: V
Synonym: 50s Ribosomal Protein L24e, Hl21hl22
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L29
Chain: W
Synonym: 50s Ribosomal Protein L29p, Hmal29, Hl33
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L30
Chain: X
Synonym: 50s Ribosomal Protein L30p, Hmal30, Hl20, Hl16
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L31e
Chain: Y
Synonym: 50s Ribosomal Protein L31e, L34, Hl30
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L32e
Chain: Z
Synonym: 50s Ribosomal Protein L32e, Hl5
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37ae
Chain: 1
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37e
Chain: 2
Synonym: 50s Ribosomal Protein L37e, L35e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L39e
Chain: 3
Synonym: 50s Ribosomal Proteins L39e, Hl39e, Hl46e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L44e
Chain: 4
Synonym: 50s Ribosomal Protein L44e, La, Hla
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.219 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
212.902 300.474 575.176 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CD, CL, K, MG, NA, TYK enzyme
related structures by homologous chain: 1KD1, 1N8R
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


C


D


E


F


G


H
  • ribonuclease P activity


    • I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceThe structures of four macrolide antibiotics bound to the large ribosomal subunit., Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA, Mol Cell 2002 Jul;10(1):117-28. PMID:12150912
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2000 Kb) [Save to disk]
  • Biological Unit Coordinates (1k9m.pdb1.gz) 1961 Kb
  • LPC: Ligand-Protein Contacts for 1K9M
  • CSU: Contacts of Structural Units for 1K9M
  • Likely Quarternary Molecular Structure file(s) for 1K9M
  • Structure Factors (5317 Kb)
  • Retrieve 1K9M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K9M from S2C, [Save to disk]
  • Re-refined 1k9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1K9M 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 1K9M
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1K9M, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k9m1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1k9m2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1k9m3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1k9m4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1k9mc2, region C:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1k9mc1, region C:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1k9md_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1k9me_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1k9mf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1k9mg1, region G:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1k9mg2, region G:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1k9mh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1k9mi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1k9mj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1k9mk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1k9ml_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1k9mm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1k9mn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1k9mo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1k9mp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1k9mq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1k9mr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1k9ms_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1k9mt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1k9mu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1k9mv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1k9mw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1k9mx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1k9my_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1k9mz_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1k9m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k9m_O] [1k9m_X] [1k9m_J] [1k9m_Z] [1k9m_I] [1k9m_B] [1k9m_M] [1k9m_2] [1k9m_E] [1k9m_3] [1k9m] [1k9m_W] [1k9m_F] [1k9m_L] [1k9m_V] [1k9m_D] [1k9m_4] [1k9m_K] [1k9m_G] [1k9m_A] [1k9m_1] [1k9m_S] [1k9m_R] [1k9m_C] [1k9m_Y] [1k9m_H] [1k9m_Q] [1k9m_T] [1k9m_P] [1k9m_N] [1k9m_U]
  • SWISS-PROT database: [P60617] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL10_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 1K9M: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
    • Other resources with information on 1K9M
  • Community annotation for 1K9M 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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