1VQM Ribosome date Dec 16, 2004
title The Structure Of The Transition State Analogue "Dan" Bound T Large Ribosomal Subunit Of Haloarcula Marismortui
authors T.M.Schmeing, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5'-R(Cpcp(Ppu)P(Po2)P(Da)Pcc)-3')
Chain: 4
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligo C-C-Puromycin-Po2-Da-C-C

Molecule: 50s Ribosomal Protein L2p
Chain: A

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L3p
Chain: B

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4e
Chain: C

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p
Chain: D

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L6p
Chain: E

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: F

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: G

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: J

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: P

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: Q

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: R

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: S

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: U

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: V

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: W

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: X

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Y

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: 1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 2

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 3

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.214 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.445 298.564 574.493 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 1MA, C, CD, CL, DA, K, MG, NA, OMG, OMU, PO2, PPU, PSU, SR, UR3 enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


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 referenceStructural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction., Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA, Mol Cell 2005 Nov 11;20(3):437-48. PMID:16285925
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2010 Kb) [Save to disk]
  • Biological Unit Coordinates (1vqm.pdb1.gz) 1974 Kb
  • LPC: Ligand-Protein Contacts for 1VQM
  • CSU: Contacts of Structural Units for 1VQM
  • Likely Quarternary Molecular Structure file(s) for 1VQM
  • Structure Factors (6843 Kb)
  • Retrieve 1VQM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VQM from S2C, [Save to disk]
  • Re-refined 1vqm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VQM 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 1VQM
  • 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 1VQM, from MSDmotif at EBI
  • Fold representative 1vqm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vqm_P] [1vqm_C] [1vqm_H] [1vqm_B] [1vqm_O] [1vqm_1] [1vqm_2] [1vqm_X] [1vqm_K] [1vqm_4] [1vqm_G] [1vqm_V] [1vqm_M] [1vqm_Q] [1vqm_Z] [1vqm_U] [1vqm_S] [1vqm_L] [1vqm_J] [1vqm_Y] [1vqm_D] [1vqm_F] [1vqm_W] [1vqm_T] [1vqm_N] [1vqm_E] [1vqm_0] [1vqm_9] [1vqm] [1vqm_3] [1vqm_I] [1vqm_A] [1vqm_R]
  • SWISS-PROT database: [P60617] [P14122] [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] [RL11_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 1VQM: [HhH1] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
  • Other resources with information on 1VQM
  • Community annotation for 1VQM 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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