1DK1	Ribosome	date	Dec 06, 1999
title	Detailed View Of A Key Element Of The Ribosome Assembly: Cry Structure Of The S15-Rrna Complex
authors	A.Nikulin, A.Serganov, E.Ennifar, S.Tischenko, N.Nevskaya
compound		source
Molecule: Rrna Fragment Chain: B Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: 30s Ribosomal Protein S15 Chain: A Fragment: Residues 2-87 Engineered: Yes Mutation: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 274 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 64 2 2	R_factor 0.213 R_Free 0.291
crystal cell	length a length b length c angle alpha angle beta angle gamma 128.800 128.800 65.100 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	K, MG, MSE, NA	enzyme
note	1DK1 is a representative structure
related structures	by homologous chain: 1F7Y, 1G1X
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structure of the S15-rRNA complex., Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W, Portier C, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P, Nat Struct Biol 2000 Apr;7(4):273-7. PMID:10742169

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk] Biological Unit Coordinates (1dk1.pdb1.gz) 42 Kb LPC: Ligand-Protein Contacts for 1DK1 CSU: Contacts of Structural Units for 1DK1 Likely Quarternary Molecular Structure file(s) for 1DK1 Retrieve 1DK1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DK1 from S2C, [Save to disk]

View 1DK1 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 1DK1

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1DK1, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dk1a_, region A [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: [1dk1_B] [1dk1] [1dk1_A] SWISS-PROT database: [P80378] Domain organization of [RS15_THETH] by SWISSPFAM Domain found in 1DK1: [Ribosomal_S15 ] by SMART

Other resources with information on 1DK1

Community annotation for 1DK1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---