5GAF Ribosome date Nov 25, 2015
title Rnc In Complex With Srp
authors A.Jomaa, D.Boehringer, M.Leibundgut, N.Ban
compound source
Molecule: Srp 4.5s Rna
Chain: 1
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Trna Ccaend
Chain: 2
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 23s Ribosomal Rna
Chain: A
Synonym: 23s Rrna
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 5s Ribosomal Rna
Chain: B
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L2
Chain: C
Synonym: Ribosomal Protein Ul2
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L3
Chain: D
Synonym: Ribosomal Protein Ul3
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L4
Chain: E
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L5
Chain: F
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L6
Chain: G
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L9
Chain: H
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L10
Chain: I
Synonym: 50s Ribosomal Protein L8
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L11
Chain: J
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L13
Chain: K
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L14
Chain: L
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L15
Chain: M
Synonym: Ribosomal Protein Ul15
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L16
Chain: N
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L17
Chain: O
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L18
Chain: P
Synonym: Ribosomal Protein Ul18
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L19
Chain: Q
Synonym: Ribosomal Protein Bl19
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L20
Chain: R
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L21
Chain: S
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L22
Chain: T
Synonym: Ribosomal Protein Ul22
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L23
Chain: U
Synonym: Ribosomal Protein Ul23
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L24
Chain: V
Synonym: Ribosomal Protein Ul24
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L25
Chain: W
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L27
Chain: X
Synonym: Ribosomal Protein Bl27
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L28
Chain: Y
Synonym: Ribosomal Protein Bl28
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L29
Chain: Z
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L30
Chain: a
Synonym: Ribosomal Protein Ul30
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L32
Chain: b
Synonym: Ribosomal Protein Bl32
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L33
Chain: c
Synonym: Ribosomal Protein Bl33
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L34
Chain: d
Synonym: Ribosomal Protein Bl34
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L35
Chain: e
Synonym: Ribosomal Protein A,Ribosomal Protein Bl35
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L36
Chain: f
Synonym: Ribosomal Protein B, Ribosomal Protein Bl36
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Signal Recognition Particle Protein
Chain: I
Synonym: Fifty-Four Homolog,Ffh,P48
Other_details: Notes: Less Defined Regions Were Replac
Unk Residues. Full Sequence Is Below: Mfdnltdrlsrtlrnisgrgrltednvkdtlrevrmalleadvalpvvrefinrvkeka Pgqefvkivrnelvaamgeenqtlnlaaqppavvlmaglqgagkttsvgklgkflrekh Vyrpaaikqletlaeqvgvdffpsdvgqkpvdivnaalkeaklkfydvllvdtagrlhv Vhasinpvetlfvvdamtgqdaantakafnealpltgvvltkvdgdarggaalsirhit Ektealepfhpdriasrilgmgdvlsliedieskvdraqaeklasklkkgdgfdlndfl Gmaslmgklpgmgqipdnvksqmddkvlvrmeaiinsmtmkerakpeiikgsrkrriaa Rllkqfddmqrmmkkmkkggmakmmrsmkgmmppgfpgr;
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 1a9l Ss
Chain: k
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.30 Å
ligand GNP, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R
  • translation repressor activi...


    • S


    T


    U


    V


    W


    X


    Y


    Z


    a


    b


    c


    d


    e


    f


    i


    Primary referenceStructures of the E. coli translating ribosome with SRP and its receptor and with the translocon., Jomaa A, Boehringer D, Leibundgut M, Ban N, Nat Commun. 2016 Jan 25;7:10471. doi: 10.1038/ncomms10471. PMID:26804923
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1643 Kb) [Save to disk]
  • Biological Unit Coordinates (5gaf.pdb1.gz) 1624 Kb
  • LPC: Ligand-Protein Contacts for 5GAF
  • CSU: Contacts of Structural Units for 5GAF
  • Retrieve 5GAF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GAF from S2C, [Save to disk]
    • View 5GAF 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 5GAF
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gaf_b] [5gaf_Q] [5gaf_O] [5gaf_R] [5gaf_K] [5gaf_L] [5gaf_f] [5gaf_I] [5gaf_S] [5gaf_d] [5gaf_B] [5gaf_D] [5gaf_C] [5gaf_Z] [5gaf_J] [5gaf_V] [5gaf_e] [5gaf_U] [5gaf_A] [5gaf_G] [5gaf_W] [5gaf_N] [5gaf_i] [5gaf_c] [5gaf_F] [5gaf_T] [5gaf_M] [5gaf_X] [5gaf] [5gaf_2] [5gaf_k] [5gaf_Y] [5gaf_E] [5gaf_P] [5gaf_a] [5gaf_1] [5gaf_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5GAF: [AAA] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [SRP54] [SRP54_N ] by SMART
    • Other resources with information on 5GAF
  • Community annotation for 5GAF at PDBWiki (http://pdbwiki.org)

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