3AGY Chaperone date Apr 12, 2010
title Crystal Structure Of Human Hsp40 Hdj1 Peptide-Binding Domain With A C-Terminal Peptide Of Hsp70
authors H.Suzuki, S.Noguchi, Y.Satow
compound source
Molecule: Dnaj Homolog Subfamily B Member 1
Chain: A, B
Fragment: Unp Residues 161-340
Synonym: Heat Shock 40 Kda Protein 1, Heat Shock Protein 40 Dnaj Protein Homolog 1, Human Dnaj Protein 1, Hdj-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dnajb1, Dnaj1, Hdj1, Hspf1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23a

Molecule: Peptide Of Heat Shock Cognate 71 Kda Protein
Chain: C, D, F
Fragment: Unp Residues 639-646
Synonym: Hsp70, Hspa1a, Heat Shock 70 Kda Protein 8
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Synthetic Peptide
symmetry Space Group: P 1 21 1
R_factor 0.225 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
104.746 41.132 62.865 90.00 97.42 90.00
method X-Ray Diffractionresolution 1.85 Å
A, B

Primary referencePeptide-binding sites as revealed by the crystal structures of the human Hsp40 Hdj1 C-terminal domain in complex with the octapeptide from human Hsp70., Suzuki H, Noguchi S, Arakawa H, Tokida T, Hashimoto M, Satow Y, Biochemistry. 2010 Oct 5;49(39):8577-84. Epub 2010 Sep 9. PMID:20809635
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (3agy.pdb1.gz) 66 Kb
  • CSU: Contacts of Structural Units for 3AGY
  • Structure Factors (881 Kb)
  • Retrieve 3AGY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AGY from S2C, [Save to disk]
  • Re-refined 3agy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AGY 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 3AGY
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3AGY, from MSDmotif at EBI
  • Fold representative 3agy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3agy_F] [3agy_C] [3agy] [3agy_A] [3agy_B] [3agy_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3AGY
  • Community annotation for 3AGY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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