1KD7 Membrane Protein date Nov 12, 2001
title Crystal Structure Of An Extracellular Domain Fragment Of Hum
authors M.Karpusas, T.G.Cachero, F.Qian, A.Boriack-Sjodin, C.Mullen, K.St M.Hsu, S.L.Kalled
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, C, K, L, M
Fragment: Extracellular Domain Fragment
Synonym: Baff, Tall-1, Tnf-And-Apol-Related Leukocyte Expre Ligand 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
symmetry Space Group: P 65
R_factor 0.217 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.720 121.720 160.740 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
related structures by homologous chain: 1OQD, 1OSG
Gene
Ontology
ChainFunctionProcessComponent
A, M, C, K, L, B


Primary referenceCrystal structure of extracellular human BAFF, a TNF family member that stimulates B lymphocytes., Karpusas M, Cachero TG, Qian F, Boriack-Sjodin A, Mullen C, Strauch K, Hsu YM, Kalled SL, J Mol Biol 2002 Feb 1;315(5):1145-54. PMID:11827482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (1kd7.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (1kd7.pdb2.gz) 67 Kb
  • CSU: Contacts of Structural Units for 1KD7
  • Likely Quarternary Molecular Structure file(s) for 1KD7
  • Structure Factors (300 Kb)
  • Retrieve 1KD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KD7 from S2C, [Save to disk]
  • Re-refined 1kd7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KD7 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 1KD7
  • 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 1KD7, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kd7a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kd7b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kd7c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kd7k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1kd7l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1kd7m_, region M [Jmol] [rasmolscript] [script source]
  • Fold representative 1kd7 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: [1kd7] [1kd7_B] [1kd7_M] [1kd7_K] [1kd7_L] [1kd7_A] [1kd7_C]
  • SWISS-PROT database: [Q9Y275]
  • Domain organization of [TN13B_HUMAN] by SWISSPFAM
  • Domain found in 1KD7: [TNF ] by SMART
  • Other resources with information on 1KD7
  • Community annotation for 1KD7 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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