1NKW Ribosome date Jan 05, 2003
title Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
authors J.M.Harms, F.Schluenzen, R.Zarivach, A.Bashan, S.Gat, I.Agmon, H.Bartels, F.Franceschi, A.Yonath
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L2
Chain: A

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L3
Chain: B

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L9
Chain: F

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L11
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L16
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: P

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: S

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: General Stress Protein Ctc
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: W

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: X

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L31
Chain: Y

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L36
Chain: 4

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
symmetry Space Group: I 2 2 2
R_factor 0.240 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
170.000 410.000 697.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
note 1NKW supersedes 1LNR, 1KPJ, 1KC9
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


W


X


Y


Z


Primary referenceHigh resolution structure of the large ribosomal subunit from a mesophilic eubacterium., Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A, Cell 2001 Nov 30;107(5):679-88. PMID:11733066
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1145 Kb) [Save to disk]
  • Biological Unit Coordinates (1nkw.pdb1.gz) 1136 Kb
  • CSU: Contacts of Structural Units for 1NKW
  • Likely Quarternary Molecular Structure file(s) for 1NKW
  • Retrieve 1NKW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NKW from S2C, [Save to disk]
  • View 1NKW 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 1NKW
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NKW, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nkw0_, region 0 [Jmol] [rasmolscript] [script source]
        - Domain d1nkw1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1nkw2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1nkw3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1nkw4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1nkw9_, region 9 [Jmol] [rasmolscript] [script source]
        - Domain d1nkwa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nkwb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nkwc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nkwd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1nkwe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1nkwf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1nkwg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1nkwh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1nkwi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1nkwj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1nkwk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1nkwl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1nkwm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1nkwn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1nkwo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1nkwp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1nkwq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1nkwr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1nkws_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1nkwt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1nkwu_, region U [Jmol] [rasmolscript] [script source]
        - Domain d1nkww_, region W [Jmol] [rasmolscript] [script source]
        - Domain d1nkwx_, region X [Jmol] [rasmolscript] [script source]
        - Domain d1nkwy_, region Y [Jmol] [rasmolscript] [script source]
        - Domain d1nkwz_, region Z [Jmol] [rasmolscript] [script source]
  • Fold representative 1nkw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nkw_D] [1nkw_R] [1nkw_I] [1nkw_A] [1nkw_C] [1nkw_L] [1nkw_U] [1nkw_K] [1nkw_Y] [1nkw_T] [1nkw_P] [1nkw_J] [1nkw_9] [1nkw_Q] [1nkw_B] [1nkw_F] [1nkw_2] [1nkw_S] [1nkw_X] [1nkw_O] [1nkw_0] [1nkw_H] [1nkw_W] [1nkw] [1nkw_N] [1nkw_Z] [1nkw_M] [1nkw_G] [1nkw_3] [1nkw_E] [1nkw_4] [1nkw_1]
  • SWISS-PROT database: [Q9RSS7] [Q9RXY1] [Q9RXJ2] [Q9RSK9] [Q9RXJ5] [Q9RSJ5] [Q9RSL2] [Q9RWB4] [Q9RSW7] [Q9RY64] [Q9RXJ7] [Q9RXK0] [Q9RXJ1] [Q9RX88] [Q9RY65] [Q9RXJ4] [Q9RXJ9] [Q9RSL0] [Q9RW44] [P49228] [Q9RSS4] [Q9RSH2] [Q9RSW6] [Q9RSK0] [Q9RXK2] [Q9RXK1] [Q9RXJ0] [Q9RSL3] [Q9RY49]
  • Domain organization of [RL11_DEIRA] [RL13_DEIRA] [RL14_DEIRA] [RL15_DEIRA] [RL16_DEIRA] [RL17_DEIRA] [RL18_DEIRA] [RL19_DEIRA] [RL20_DEIRA] [RL21_DEIRA] [RL22_DEIRA] [RL23_DEIRA] [RL24_DEIRA] [RL25_DEIRA] [RL27_DEIRA] [RL29_DEIRA] [RL2_DEIRA] [RL30_DEIRA] [RL31_DEIRA] [RL32_DEIRA] [RL33_DEIRA] [RL34_DEIRA] [RL35_DEIRA] [RL36_DEIRA] [RL3_DEIRA] [RL4_DEIRA] [RL5_DEIRA] [RL6_DEIRA] [RL9_DEIRA] by SWISSPFAM
  • Domains found in 1NKW: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 1NKW
  • Community annotation for 1NKW 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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