1Q7Y Ribosome date Aug 20, 2003
title Crystal Structure Of Ccdap-Puromycin Bound At The Peptidyl T Center Of The 50s Ribosomal Subunit
authors J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain: A
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: B

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ccda-P-Puromycin
Chain: 5
Engineered: Yes
Other_details: Peptidyl Transferase Intermediate Analogue C Puromycin;

Synthetic: Yes
Other_details: Ccda-P-Puromycin Synthesised By Michael Yaru Unviversity Of Colorado At Boulder;

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: H
Synonym: Hs6

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: I
Synonym: L10e, Hmal10

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L10 Ribosomal Protein
Chain: J

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: K

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: L
Synonym: Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L15 Ribosomal Protein
Chain: N

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: R
Synonym: Hl31

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: V
Synonym: Hl21hl22

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

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

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Z
Synonym: Hl5

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: L37ae 50s Ribosomal Protein
Chain: 1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: 2
Synonym: L35e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 3
Synonym: Hl39e, Hl46e

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 4
Synonym: La, Hla

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.280
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 3.20 Å
ligand CD, CL, K, MG, NA, PO4, PUY enzyme
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 referenceStructural insights into peptide bond formation., Hansen JL, Schmeing TM, Moore PB, Steitz TA, Proc Natl Acad Sci U S A 2002 Sep 3;99(18):11670-5. PMID:12185246
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1996 Kb) [Save to disk]
  • Biological Unit Coordinates (1q7y.pdb1.gz) 1962 Kb
  • LPC: Ligand-Protein Contacts for 1Q7Y
  • CSU: Contacts of Structural Units for 1Q7Y
  • Likely Quarternary Molecular Structure file(s) for 1Q7Y
  • Structure Factors (3410 Kb)
  • Retrieve 1Q7Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q7Y from S2C, [Save to disk]
  • Re-refined 1q7y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q7Y 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 1Q7Y
  • 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 1Q7Y, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q7y1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1q7y2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1q7y3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1q7y4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1q7yc2, region C:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1q7yc1, region C:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1q7yd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1q7ye_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1q7yf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1q7yg1, region G:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1q7yg2, region G:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1q7yh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1q7yi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1q7yj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1q7yk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1q7yl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1q7ym_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1q7yn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1q7yo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1q7yp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1q7yq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1q7yr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1q7ys_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1q7yt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1q7yu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1q7yv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1q7yw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1q7yx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1q7yy_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1q7yz_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1q7y 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: [1q7y] [1q7y_T] [1q7y_J] [1q7y_4] [1q7y_M] [1q7y_N] [1q7y_B] [1q7y_Y] [1q7y_K] [1q7y_I] [1q7y_5] [1q7y_3] [1q7y_E] [1q7y_P] [1q7y_U] [1q7y_L] [1q7y_V] [1q7y_G] [1q7y_A] [1q7y_Q] [1q7y_W] [1q7y_O] [1q7y_S] [1q7y_X] [1q7y_C] [1q7y_R] [1q7y_1] [1q7y_2] [1q7y_H] [1q7y_F] [1q7y_Z] [1q7y_D]
  • 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 1Q7Y: [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 1Q7Y
  • Community annotation for 1Q7Y 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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