1PYB	Rna Binding Protein	date	Jul 08, 2003
title	Crystal Structure Of Aquifex Aeolicus Trbp111: A Structure-S Trna Binding Protein
authors	M.A.Swairjo, A.J.Morales, C.C.Wang, A.R.Ortiz, P.Schimmel
compound		source
Molecule: Trna-Binding Protein Trbp111 Chain: A, B, C, D Engineered: Yes		Organism_scientific: Aquifex Aeolicus Organism_taxid: 63363 Gene: Metg Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Tg1 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ptsmg32
symmetry	Space Group: C 1 2 1	R_factor 0.208 R_Free 0.226
crystal cell	length a length b length c angle alpha angle beta angle gamma 145.400 72.790 68.940 90.00 91.93 90.00
method	X-Ray Diffraction	resolution	2.50 Å
note	1PYB is a representative structure
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Crystal structure of trbp111: a structure-specific tRNA-binding protein., Swairjo MA, Morales AJ, Wang CC, Ortiz AR, Schimmel P, EMBO J. 2000 Dec 1;19(23):6287-98. PMID:11101501

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk] Biological Unit Coordinates (1pyb.pdb1.gz) 32 Kb Biological Unit Coordinates (1pyb.pdb2.gz) 32 Kb CSU: Contacts of Structural Units for 1PYB Likely Quarternary Molecular Structure file(s) for 1PYB Structure Factors (265 Kb) Retrieve 1PYB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1PYB from S2C, [Save to disk] Re-refined 1pyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1PYB 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 1PYB

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 1PYB, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1pyba_, region A [Jmol] [rasmolscript] [script source]     - Domain d1pybb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1pybc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1pybd_, region D [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: [1pyb_D] [1pyb_B] [1pyb_C] [1pyb_A] [1pyb] SWISS-PROT database: [O66738] Domain organization of [O66738_AQUAE] by SWISSPFAM

Other resources with information on 1PYB

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

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