5JVH Ribosome date May 11, 2016
title The Crystal Structure Large Ribosomal Subunit (50s) Of Deino Radiodurans In Complex With Evernimicin
authors A.Yonath
compound source
Molecule: 23s Ribosomal Rna
Chain: X
Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 5s Ribosomal Rna
Chain: Y

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L2
Chain: A

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L3
Chain: B
Other_details: Deinococcus

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L13
Chain: G

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L14
Chain: H

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L15
Chain: I

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L16
Chain: J

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L17
Chain: K

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L18
Chain: L

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L19
Chain: M

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L20
Chain: N

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L21
Chain: O

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L22
Chain: P

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L23
Chain: Q

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L24
Chain: R

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L27
Chain: T

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L28
Chain: U

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L29
Chain: V

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L30
Chain: W

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230
symmetry Space Group: I 2 2 2
R_factor 0.204 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.475 407.380 692.552 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.58 Å
ligand 6O1, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3531 Kb) [Save to disk]
  • Biological Unit Coordinates (5jvh.pdb1.gz) 3514 Kb
  • LPC: Ligand-Protein Contacts for 5JVH
  • CSU: Contacts of Structural Units for 5JVH
  • Structure Factors (3278 Kb)
  • Retrieve 5JVH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JVH from S2C, [Save to disk]
  • Re-refined 5jvh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5JVH 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 5JVH
  • 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
  • Fold representative 5jvh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jvh_2] [5jvh_P] [5jvh_O] [5jvh_1] [5jvh_D] [5jvh_T] [5jvh_A] [5jvh_3] [5jvh_Q] [5jvh_S] [5jvh_X] [5jvh_W] [5jvh] [5jvh_M] [5jvh_K] [5jvh_H] [5jvh_U] [5jvh_N] [5jvh_G] [5jvh_E] [5jvh_B] [5jvh_R] [5jvh_Y] [5jvh_V] [5jvh_Z] [5jvh_L] [5jvh_J] [5jvh_I] [5jvh_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JVH: [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 5JVH
  • Community annotation for 5JVH at PDBWiki (http://pdbwiki.org)

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