2P7E	Rna	date	Mar 20, 2007
title	Vanadate At The Active Site Of A Small Ribozyme Suggests A R Water In Transition-State Stabilization
authors	A.T.Torelli, J.Krucinska, J.E.Wedekind
compound		source
Molecule: 5' Substrate Strand, Pentameric Fragment Chain: A Engineered: Yes Other_details: Vanadium Oxide At The 2' And 3' Oxygens Of T A;		Synthetic: Yes Other_details: Sequence Occurs Naturally In Tobacco Ringspo Satellite Rna;
Molecule: Ribozyme Strand I Chain: B Engineered: Yes Other_details: Domain-Linking Residue S9l At The 3'-End		Synthetic: Yes Other_details: Sequence Occurs Naturally In Tobacco Ringspo Satellite Rna;
Molecule: Ribozyme Strand II Chain: C Engineered: Yes Other_details: Domain-Linking Residue S9l At The 5'-End		Synthetic: Yes Other_details: Sequence Occurs Naturally In Tobacco Ringspo Satellite Rna;
Molecule: Ribozyme Strand III Chain: D Engineered: Yes Other_details: Contains The S-Turn		Synthetic: Yes Other_details: Sequence Occurs Naturally In Tobacco Ringspo Satellite Rna;
Molecule: 3' Substrate Strand, Octameric Fragment Chain: P Engineered: Yes Other_details: Vanadium Oxide At The O5' Oxygen Of The 5'-E		Synthetic: Yes Other_details: Sequence Occurs Naturally In Tobacco Ringspo Satellite Rna
symmetry	Space Group: P 61 2 2	R_factor 0.258 R_Free 0.271
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.100 94.100 132.400 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.05 Å
ligand	AVC, NCO, S9L, SO4	enzyme
Primary reference	A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization., Torelli AT, Krucinska J, Wedekind JE, RNA. 2007 May 8;. PMID:17488874

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (34 Kb) [Save to disk] Biological Unit Coordinates (2p7e.pdb1.gz) 29 Kb LPC: Ligand-Protein Contacts for 2P7E CSU: Contacts of Structural Units for 2P7E Likely Quarternary Molecular Structure file(s) for 2P7E Structure Factors (300 Kb) Retrieve 2P7E in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2P7E from S2C, [Save to disk] Re-refined 2p7e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2P7E 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 2P7E

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 2P7E, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2p7e_A] [2p7e_D] [2p7e_B] [2p7e_P] [2p7e_C] [2p7e] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 2P7E

Community annotation for 2P7E at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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