1W2B Ribosome date Jul 01, 2004
title Trigger Factor Ribosome Binding Domain In Complex With 50s
authors L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban
compound source
Molecule: 23s Rrna
Chain
 Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 1
Synonym: Hl39e, Hl46e, Ribosomal Protein L39e
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e La, Hla, Ribosomal Pro
Chain: 2
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: Trigger Factor
Chain: 5
Fragment: N-Terminal Ribosome Binding Fragment, Residues 1-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5s Rrna
Chain: 9
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

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

Molecule: 50s Ribosomal Protein L4p
Chain: C
Synonym: Ribosomal Protein L4, Hmal4, Hl6
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p Hmal5, Hl13, Ribosomal L5;
Chain: D
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Synonym: Hs6, Ribosomal Protein L10
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: G
Synonym: Ribosomal Protein L10, Acidic Ribosomal Protein P0 L10e, Hmal10;
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H
Synonym: Ribosomal Protein L10e
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

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

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

Molecule: 50s Ribosomal Protein L15e
Chain: L
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

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

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

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

Molecule: 50s Ribosomal Protein L22p Hmal22, Hl23, Ribosoma L22;
Chain: Q
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

Molecule: Ribosomal Protein L24
Chain: S
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T
Synonym: Hmal24, Hl16, Hl15, Ribosomal Protein L24p
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

Molecule: 50s Ribosomal Protein L30p
Chain: V
Synonym: Hmal30, Hl20, Hl16 Ribosomal Protein L29
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

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

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

Molecule: 50s Ribosomal Protein L37ae
Chain: Y
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238

Molecule: Ribosomal Protein L37e
Chain: Z
Synonym: L35e
Organism_scientific: Haloarcula Marismortui
Organism_common: Archaea
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.192 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
210.746 298.871 574.173 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand CD, CL, K, MG, NA enzyme
note 1W2B is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
1


2


5


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 referenceTrigger factor in complex with the ribosome forms a molecular cradle for nascent proteins., Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N, Nature. 2004 Sep 30;431(7008):590-6. Epub 2004 Aug 29. PMID:15334087
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1945 Kb) [Save to disk]
  • Biological Unit Coordinates (1w2b.pdb1.gz) 1910 Kb
  • LPC: Ligand-Protein Contacts for 1W2B
  • CSU: Contacts of Structural Units for 1W2B
  • Likely Quarternary Molecular Structure file(s) for 1W2B
  • Retrieve 1W2B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1W2B from S2C, [Save to disk]
    • View 1W2B 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 1W2B
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1W2B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1w2b1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1w2b2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1w2b5_, region 5 [Jmol] [rasmolscript] [script source]
        - Domain d1w2ba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1w2bb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1w2bc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1w2bd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1w2be_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1w2bf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1w2bg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1w2bh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1w2bi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1w2bj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1w2bk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1w2bl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1w2bm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1w2bn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1w2bo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1w2bp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1w2br_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1w2bs_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1w2bt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1w2bu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1w2bv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1w2bw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1w2bx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1w2by_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1w2bz_, region Z [Jmol] [rasmolscript] [script source]
  • 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: [1w2b_Z] [1w2b_2] [1w2b_R] [1w2b_W] [1w2b_M] [1w2b_S] [1w2b_F] [1w2b_0] [1w2b_U] [1w2b_9] [1w2b_C] [1w2b_X] [1w2b_K] [1w2b_L] [1w2b_Q] [1w2b_V] [1w2b_T] [1w2b_G] [1w2b_B] [1w2b_O] [1w2b_N] [1w2b_H] [1w2b_E] [1w2b_P] [1w2b_5] [1w2b] [1w2b_A] [1w2b_J] [1w2b_Y] [1w2b_D] [1w2b_I] [1w2b_1]
  • 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] [P0A850]
  • 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] [TIG_ECOLI] by SWISSPFAM
  • Domains found in 1W2B: [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 1W2B
  • Community annotation for 1W2B at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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