1D00 Apoptosis date Sep 07, 1999
title Structure Of Tnf Receptor Associated Factor 2 In Complex With A 5-Residue Cd40 Peptide
authors H.Ye, Y.C.Park, M.Kreishman, E.Kieff, H.Wu
compound source
Molecule: Tumor Necrosis Factor Receptor Associated Protein 2;
Chain: A, B, C, D, E, F, G, H
Fragment: Traf Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24d

Molecule: B-Cell Surface Antigen Cd40
Chain: I, J, K, L, M, N, O, P
Fragment: Acetylated 5-Residue Peptide
Engineered: Yes

Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized. The Sequence Of This Peptide Naturally Occurs In Humans (Homo Sapiens)
symmetry Space Group: R 3
R_factor 0.219 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.400 111.400 111.400 103.70 103.70 103.70
method X-Ray Diffractionresolution 2.00 Å
ligand ACE, NH2 enzyme
related structures by homologous chain: 1CZY, 1D01
Primary referenceThe structural basis for the recognition of diverse receptor sequences by TRAF2., Ye H, Park YC, Kreishman M, Kieff E, Wu H, Mol Cell 1999 Sep;4(3):321-30. PMID:10518213
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (214 Kb) [Save to disk]
  • Biological Unit Coordinates (1d00.pdb1.gz) 81 Kb
  • Biological Unit Coordinates (1d00.pdb2.gz) 81 Kb
  • Biological Unit Coordinates (1d00.pdb3.gz) 81 Kb
  • Biological Unit Coordinates (1d00.pdb4.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 1D00
  • CSU: Contacts of Structural Units for 1D00
  • Likely Quarternary Molecular Structure file(s) for 1D00
  • Retrieve 1D00 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D00 from S2C, [Save to disk]
  • View 1D00 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 1D00
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D00, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d00a2, region A:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00a1, region A:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00b2, region B:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00b1, region B:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00c2, region C:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00c1, region C:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00d2, region D:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00d1, region D:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00e2, region E:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00e1, region E:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00f2, region F:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00f1, region F:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00g2, region G:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00g1, region G:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d00h2, region H:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d00h1, region H:350-501 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d00 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1d00_J] [1d00_E] [1d00_K] [1d00_M] [1d00_N] [1d00_L] [1d00_D] [1d00_I] [1d00_A] [1d00_H] [1d00_O] [1d00_P] [1d00_G] [1d00_C] [1d00] [1d00_F] [1d00_B]
  • SWISS-PROT database: [P25942] [Q12933]
  • Domain organization of [TNR5_HUMAN] [TRAF2_HUMAN] by SWISSPFAM
  • Domain found in 1D00: [MATH ] by SMART
  • Other resources with information on 1D00
  • Community annotation for 1D00 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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