1D01 Apoptosis date Sep 07, 1999
title Structure Of Tnf Receptor Associated Factor 2 In Complex With A Human Cd30 Peptide
authors H.Ye, Y.C.Park, M.Kreishman, E.Kieff, H.Wu
compound source
Molecule: Tumor Necrosis Factor Receptor Associated Factor 2;
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 Sequence Of This Peptide Naturally Occurs In Humans (Homo Sapiens)
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.244
crystal
cell
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
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
  • Alignments of the sequence of 1D01 with the sequences similar proteins can be viewed for 1D01's classification [TNR8_HUMAN] [TRAF2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [TNR8_HUMAN] [TRAF2_HUMAN] at ProtoMap. Click on the Cluster number.
  • 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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