1NJI Ribosome date Dec 31, 2002
title Structure Of Chloramphenicol Bound To The 50s Ribosomal Subu
authors J.L.Hansen, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain: A
 Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 5s Ribosomal Rna
Chain: B
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L2p
Chain: C
Synonym: Hmal2, Hl4
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L3p
Chain: D
Synonym: Hmal3, Hl1
Mutation: Yes
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L4e
Chain: E
Synonym: Hmal4, Hl6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L5p
Chain: F
Synonym: Hmal5, Hl13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L6p
Chain: G
Synonym: Hmal6, Hl10
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L7ae
Chain: H
Synonym: Hs6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: I
Synonym: L10e, Hmal10
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L10e
Chain: J
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L13p
Chain: K
Synonym: Hmal13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L14p
Chain: L
Synonym: Hmal14, Hl27
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L15p
Chain: M
Synonym: Hmal15, Hl9
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L15e
Chain: N
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L18p
Chain: O
Synonym: Hmal18, Hl12
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L18e
Chain: P
Synonym: Hl29, L19
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L19e
Chain: Q
Synonym: Hmal19, Hl24
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L21e
Chain: R
Synonym: Hl31
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L22p
Chain: S
Synonym: Hmal22, Hl23
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L23p
Chain: T
Synonym: Hmal23, Hl25, L21
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L24p
Chain: U
Synonym: Hmal24, Hl16, Hl15
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L24e
Chain: V
Synonym: Hl21hl22
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L29p
Chain: W
Synonym: Hmal29, Hl33
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L30p
Chain: X
Synonym: Hmal30, Hl20, Hl16
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L31e
Chain: Y
Synonym: L34, Hl30
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L32e
Chain: Z
Synonym: Hl5
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L37ae
Chain: 1
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L37e
Chain: 2
Synonym: L35e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L39e
Chain: 3
Synonym: Hl39e, Hl46e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells

Molecule: 50s Ribosomal Protein L44e
Chain: 4
Synonym: La, Hla
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Cultured Cells
symmetry Space Group: C 2 2 21
R_factor 0.176 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.720 299.750 573.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CD, CL, CLM, K, MG, NA enzyme
note 1NJI (Molecule of the Month:pdb121)
related structures by homologous chain: 1N8R, 1Q82, 1YJN
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 referenceStructures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit., Hansen JL, Moore PB, Steitz TA, J Mol Biol 2003 Jul 25;330(5):1061-75. PMID:12860128
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1960 Kb) [Save to disk]
  • Biological Unit Coordinates (1nji.pdb1.gz) 1926 Kb
  • LPC: Ligand-Protein Contacts for 1NJI
  • CSU: Contacts of Structural Units for 1NJI
  • Likely Quarternary Molecular Structure file(s) for 1NJI
  • Structure Factors (5621 Kb)
  • Retrieve 1NJI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NJI from S2C, [Save to disk]
  • Re-refined 1nji structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NJI 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 1NJI
  • 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
  • 3D motif for 1NJI, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nji1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1nji2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1nji3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1nji4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1njic2, region C:1-90 [Jmol] [rasmolscript] [script source]
        - Domain d1njic1, region C:91-237 [Jmol] [rasmolscript] [script source]
        - Domain d1njid_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1njie_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1njif_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1njig1, region G:1-79 [Jmol] [rasmolscript] [script source]
        - Domain d1njig2, region G:80-172 [Jmol] [rasmolscript] [script source]
        - Domain d1njih_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1njii_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1njij_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1njik_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1njil_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1njim_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1njin_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1njio_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1njip_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1njiq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1njir_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1njis_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1njit_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1njiu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1njiv_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1njiw_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1njix_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1njiy_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1njiz_, 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: [1nji_F] [1nji_Y] [1nji_B] [1nji_S] [1nji_P] [1nji_U] [1nji_3] [1nji_X] [1nji_H] [1nji] [1nji_O] [1nji_1] [1nji_2] [1nji_E] [1nji_L] [1nji_Q] [1nji_Z] [1nji_N] [1nji_C] [1nji_J] [1nji_G] [1nji_I] [1nji_R] [1nji_A] [1nji_K] [1nji_V] [1nji_M] [1nji_D] [1nji_T] [1nji_W] [1nji_4]
  • 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 1NJI: [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 1NJI
  • Community annotation for 1NJI 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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