486D	Ribosome	date	Sep 09, 1999
title	X-Ray Crystal Structures Of 70s Ribosome Functional Complexe
authors	J.H.Cate, M.M.Yusupov, G.Zh.Yusupova, T.N.Earnest, H.F.Noller
compound		source
Molecule: P-Site Trna Of 70s Ribosome Chain: A		Organism_scientific: Escherichia Coli Organism_taxid: 562
Molecule: P-Site Codon Of 70s Ribosome Chain: B Engineered: Yes		Synthetic: Yes Other_details: Sequence From T. Thermophilus
Molecule: A-Site Trna Of 70s Ribosome Chain: C		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: A-Site Codon Of 70s Ribosome Chain: D Engineered: Yes		Synthetic: Yes Other_details: Sequence From T. Thermophilus
Molecule: E-Site Trna Of 70s Ribosome Chain: E		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: Penultimate Stem Of 16s Rrna In The 70s Ribosome Chain: F		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
Molecule: 900 Stem-Loop Of 16s Rrna In The 70s Ribosome Chain: G		Organism_scientific: Thermus Thermophilus Organism_taxid: 274
symmetry	Space Group: I 4 2 2	R_factor R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 508.020 508.020 802.790 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	7.50 Å
ligand	1MA, 1MG, 2MG, 5MC, 5MU, 7MG, H2U, IR, M2G, OMC, PSU, YYG	enzyme
Primary reference	X-ray crystal structures of 70S ribosome functional complexes., Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF, Science 1999 Sep 24;285(5436):2095-104. PMID:10497122

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk] Biological Unit Coordinates (486d.pdb1.gz) 83 Kb LPC: Ligand-Protein Contacts for 486D CSU: Contacts of Structural Units for 486D Likely Quarternary Molecular Structure file(s) for 486D Retrieve 486D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 486D from S2C, [Save to disk]

View 486D 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 486D

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 486D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d486da_, region A [Jmol] [rasmolscript] [script source]     - Domain d486db_, region B [Jmol] [rasmolscript] [script source]     - Domain d486dc_, region C [Jmol] [rasmolscript] [script source]     - Domain d486dd_, region D [Jmol] [rasmolscript] [script source]     - Domain d486de_, region E [Jmol] [rasmolscript] [script source]     - Domain d486df_, region F [Jmol] [rasmolscript] [script source]     - Domain d486dg_, region G [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [486d_C] [486d_A] [486d] [486d_F] [486d_D] [486d_E] [486d_B] [486d_G] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 486D

Community annotation for 486D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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