1D01 Apoptosis date Sep 07, 1999
title Structure Of Tnf Receptor Associated Factor 2 In Complex Wit Cd30 Peptide
authors H.Ye, Y.C.Park, M.Kreishman, E.Kieff, H.Wu
compound source
Molecule: Tumor Necrosis Factor Receptor Associated Factor
Chain: A, B, C, D, E, F
Fragment: Traf Domain
Synonym: Traf2
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: Cd30 Peptide
Chain: G, H, I
Fragment: Traf-Binding Sequence
Engineered: Yes

Synthetic: Yes
Other_details: This Peptide Was Chemically Synthesized. The Of This Peptide Naturally Occurs In Humans (Homo Sapiens)
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.244
length a length b length c angle alpha angle beta angle gamma
91.300 110.400 91.300 90.00 120.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ACE enzyme
related structures by homologous chain: 1D00, 1D0A
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
F, A, D, C, E, B

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] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (1d01.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (1d01.pdb2.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 1D01
  • CSU: Contacts of Structural Units for 1D01
  • Likely Quarternary Molecular Structure file(s) for 1D01
  • Structure Factors (961 Kb)
  • Retrieve 1D01 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D01 from S2C, [Save to disk]
  • Re-refined 1d01 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D01 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 1D01
  • 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 1D01, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d01a2, region A:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01a1, region A:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d01b2, region B:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01b1, region B:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d01c2, region C:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01c1, region C:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d01d2, region D:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01d1, region D:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d01e2, region E:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01e1, region E:350-501 [Jmol] [rasmolscript] [script source]
        - Domain d1d01f2, region F:334-349 [Jmol] [rasmolscript] [script source]
        - Domain d1d01f1, region F:350-501 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d01 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: [1d01_D] [1d01] [1d01_I] [1d01_B] [1d01_A] [1d01_C] [1d01_H] [1d01_E] [1d01_F] [1d01_G]
  • SWISS-PROT database: [P28908] [Q12933]
  • Domain organization of [TNR8_HUMAN] [TRAF2_HUMAN] by SWISSPFAM
  • Domain found in 1D01: [MATH ] by SMART
  • Other resources with information on 1D01
  • Community annotation for 1D01 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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