3DPP	Chaperone, Peptide Binding Protein	date	Jul 09, 2008
title	Crystal Structure Of The Substrate Binding Domain Of E. Coli Complex With A Long Pyrrhocoricin-Derived Inhibitor Peptide
authors	A.Roujeinikova
compound		source
Molecule: Chaperone Protein Dnak Chain: A, B Fragment: Substrate Binding Domain (Unp Residues 389 To 607 Synonym: Heat Shock Protein 70, Heat Shock 70 Kda Protein, Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 83333 Gene: Dnak, Grop, Grpf, Seg, B0014, Jw0013 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3)
Molecule: Inhibitor Peptide Chain: C, D Engineered: Yes		Synthetic: Yes Other_details: The Peptide Was Pyrrhocoricin-Derived.
symmetry	Space Group: P 21 21 2	R_factor 0.237 R_Free 0.316
crystal cell	length a length b length c angle alpha angle beta angle gamma 77.870 159.120 44.790 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	ALC, SO4	enzyme
Gene Ontology	Chain Function Process Component D, C
Primary reference	Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies., Liebscher M, Roujeinikova A, J Bacteriol. 2009 Mar;191(5):1456-62. Epub 2008 Dec 19. PMID:19103929

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk] Biological Unit Coordinates (3dpp.pdb1.gz) 37 Kb Biological Unit Coordinates (3dpp.pdb2.gz) 39 Kb LPC: Ligand-Protein Contacts for 3DPP CSU: Contacts of Structural Units for 3DPP Likely Quarternary Molecular Structure file(s) for 3DPP Structure Factors (333 Kb) Retrieve 3DPP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DPP from S2C, [Save to disk] Re-refined 3dpp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DPP 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 3DPP

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3DPP, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dpp] [3dpp_B] [3dpp_A] [3dpp_C] [3dpp_D] SWISS-PROT database: [P0A6Y8] [P37362] Belongs to the cation channel-forming heat shock protein-70 (hsp70) family according to TCDB. Domain organization of [DNAK_ECOLI] [PYRRH_PYRAP] by SWISSPFAM

Other resources with information on 3DPP

Community annotation for 3DPP at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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