1JD5 Hydrolase Peptide date Jun 12, 2001
title Crystal Structure Of Diap1-Bir2grim
authors J.W.Wu, A.E.Cocina, J.Chai, B.A.Hay, Y.Shi
compound source
Molecule: Apoptosis 1 Inhibitor
Chain: A
Synonym: Diap1
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Diap1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: Cell Death Protein Grim
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized. The Is Naturally Found In Drosophila Melanogaster (Fruit Fly).
symmetry Space Group: P 65 2 2
R_factor 0.202 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.700 62.700 130.700 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand ZN enzyme
related structures by homologous chain: 1Q4Q
Primary referenceStructural analysis of a functional DIAP1 fragment bound to grim and hid peptides., Wu JW, Cocina AE, Chai J, Hay BA, Shi Y, Mol Cell 2001 Jul;8(1):95-104. PMID:11511363
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (23 Kb) [Save to disk]
  • Biological Unit Coordinates (1jd5.pdb1.gz) 19 Kb
  • LPC: Ligand-Protein Contacts for 1JD5
  • CSU: Contacts of Structural Units for 1JD5
  • Likely Quarternary Molecular Structure file(s) for 1JD5
  • Retrieve 1JD5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JD5 from S2C, [Save to disk]
  • View 1JD5 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 1JD5
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1JD5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jd5a_, 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: [1jd5_A] [1jd5] [1jd5_B]
  • SWISS-PROT database: [Q24570] [Q24306]
  • Domain organization of [GRIM_DROME] [IAP1_DROME] by SWISSPFAM
  • Domain found in 1JD5: [BIR ] by SMART
  • Other resources with information on 1JD5
  • Community annotation for 1JD5 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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