1KQS Ribosome date Jan 07, 2002
title The Haloarcula Marismortui 50s Complexed With A Pretranslocational Intermediate In Protein Synthesis
authors T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Rrna
Chain
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Rrna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Cca
Chain: 3
Engineered: Yes
Other_details: Rna Analogue Of 3' Of Deacylated-Trna

Synthetic: Yes
Other_details: Solid Phase Synthesis

Molecule: Cc-Pmn-Pcb
Chain: 4
Engineered: Yes
Other_details: An Analogue Of Peptidyl-Trna Contains Puromycin-5'-Monophosphate, Phenylalaninal, 6- Aminohexanoic Acid, And Biotin;

Synthetic: Yes
Other_details: Solid Phase Synthesis, Followed By Peptidyl Transferase Reaction.;

Molecule: Ribosomal Protein L2
Chain: A
Synonym: 50s Ribosomal Protein L2p, Hmal2, Hl4

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L3
Chain: B
Synonym: 50s Ribosomal Protein L3p, Hmal3, Hl1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L4
Chain: C
Synonym: 50s Ribosomal Protein L4e, Hmal4, Hl6

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L5
Chain: D
Synonym: 50s Ribosomal Protein L5p, Hmal5, Hl13

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L6
Chain: E
Synonym: 50s Ribosomal Protein L6p, Hmal6, Hl10

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L7ae
Chain: F
Synonym: 30s Ribosomal Protein Hs6

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10
Chain: G
Synonym: 50s Ribosomal Protein P0, Hmal10, L10e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L13
Chain: I
Synonym: 50s Ribosomal Protein L13p, Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L14
Chain: J
Synonym: 50s Ribosomal Protein L14p, Hmal14, Hl27

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15
Chain: K
Synonym: 50s Ribosomal Protein L15p, Hmal15, Hl9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15e
Chain: L

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18
Chain: M
Synonym: 50s Ribosomal Protein L18p, Hmal18, Hl12

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18e
Chain: N
Synonym: 50s Ribosomal Protein L18e, Hl29, L19

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L19e
Chain: O
Synonym: 50s Ribosomal Protein L19e, Hmal19, Hl24

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L21e
Chain: P
Synonym: 50s Ribosomal Protein L21e, Hl31

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L22
Chain: Q
Synonym: 50s Ribosomal Protein L22p, Hmal22, Hl23

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L23
Chain: R
Synonym: 50s Ribosomal Protein L23p, Hmal23, Hl25, L21

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24
Chain: S
Synonym: 50s Ribosomal Protein L24p, Hmal24, Hl16, Hl15

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24e
Chain: T
Synonym: 50s Ribosomal Protein L24e, Hl21hl22

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L29
Chain: U
Synonym: 50s Ribosomal Protein L29p, Hmal29, Hl33

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L30
Chain: V
Synonym: 50s Ribosomal Protein L30p, Hmal30, Hl20, Hl16

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L31e
Chain: W
Synonym: 50s Ribosomal Protein L31e, L34, Hl30

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L32e
Chain: X
Synonym: 50s Ribosomal Protein L32e, Hl5

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37ae
Chain: Y

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37e
Chain: Z
Synonym: 50s Ribosomal Protein L37e, L35e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L39e
Chain: 1
Synonym: 50s Ribosomal Proteins L39e, Hl39e, Hl46e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L44e
Chain: 2
Synonym: 50s Ribosomal Protein L44e, La, Hla

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.173 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
212.784 300.349 574.961 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand ACA, BTN, CD, CL, K, MG, NA, PHA, PPU enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


A


B


C


D


E


F
  • ribonuclease P activity


  • G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceA pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits., Schmeing TM, Seila AC, Hansen JL, Freeborn B, Soukup JK, Scaringe SA, Strobel SA, Moore PB, Steitz TA, Nat Struct Biol 2002 Mar;9(3):225-30. PMID:11828326
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2004 Kb) [Save to disk]
  • Biological Unit Coordinates (1kqs.pdb1.gz) 1966 Kb
  • LPC: Ligand-Protein Contacts for 1KQS
  • CSU: Contacts of Structural Units for 1KQS
  • Likely Quarternary Molecular Structure file(s) for 1KQS
  • Structure Factors (2587 Kb)
  • Retrieve 1KQS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KQS from S2C, [Save to disk]
  • Re-refined 1kqs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KQS 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 1KQS
  • 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 1KQS, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kqs1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1kqs2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1kqsa2, region A:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1kqsa1, region A:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1kqsb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kqsc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kqsd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1kqse1, region E:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1kqse2, region E:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1kqsf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1kqsg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1kqsh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1kqsi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1kqsj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1kqsk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1kqsl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1kqsm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1kqsn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1kqso_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1kqsp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1kqsq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1kqsr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1kqss_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1kqst_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1kqsu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1kqsv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1kqsw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1kqsx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1kqsy_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1kqsz_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1kqs 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: [1kqs_Q] [1kqs_G] [1kqs_U] [1kqs_T] [1kqs_1] [1kqs_4] [1kqs_K] [1kqs_C] [1kqs_3] [1kqs_M] [1kqs_J] [1kqs_R] [1kqs_E] [1kqs_N] [1kqs_Y] [1kqs_D] [1kqs_2] [1kqs_B] [1kqs_X] [1kqs_S] [1kqs_O] [1kqs] [1kqs_V] [1kqs_L] [1kqs_P] [1kqs_W] [1kqs_H] [1kqs_0] [1kqs_I] [1kqs_F] [1kqs_A] [1kqs_Z] [1kqs_9]
  • 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 1KQS: [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 1KQS
  • Community annotation for 1KQS 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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