1OQD Immune Response date Mar 07, 2003
title Crystal Structure Of Stall-1 And Bcma
authors G.Zhang
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 13b, Soluble Form;
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Extracellular Domain
Synonym: Tnf-And Apol- Related Leukocyte Expressed Ligand 1, Tall-1, B Lymphocyte Stimulator, Blys, B Cell- Activating Factor, Baff, Dendritic Cell- Derived Tnf-Like Molecule;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tumor Necrosis Factor Receptor Superfamily Member 17;
Chain: K, L, M, N, O, P, Q, R
Fragment: Extracellular Domain
Synonym: B-Cell Maturation Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 63 2 2
R_factor 0.240 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
232.854 232.854 212.477 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
related structures by homologous chain: 1KD7, 1OQE, 1XU2
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, E, B, H, C, D, I, G


Primary referenceLigand-receptor binding revealed by the TNF family member TALL-1., Liu Y, Hong X, Kappler J, Jiang L, Zhang R, Xu L, Pan CH, Martin WE, Murphy RC, Shu HB, Dai S, Zhang G, Nature 2003 May 1;423(6935):49-56. PMID:12721620
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (285 Kb) [Save to disk]
  • Biological Unit Coordinates (1oqd.pdb1.gz) 1640 Kb
  • CSU: Contacts of Structural Units for 1OQD
  • Likely Quarternary Molecular Structure file(s) for 1OQD
  • Structure Factors (637 Kb)
  • Retrieve 1OQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OQD from S2C, [Save to disk]
  • Re-refined 1oqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1OQD 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 1OQD
  • 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 1OQD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1oqda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1oqdb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1oqdc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1oqdd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1oqde_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1oqdf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1oqdg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1oqdh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1oqdi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1oqdj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1oqdk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1oqdl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1oqdm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1oqdn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1oqdo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1oqdp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1oqdq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1oqdr_, region R [Jmol] [rasmolscript] [script source]
  • Fold representative 1oqd 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: [1oqd_B] [1oqd_M] [1oqd_H] [1oqd_L] [1oqd_R] [1oqd_C] [1oqd_P] [1oqd_K] [1oqd_Q] [1oqd] [1oqd_I] [1oqd_F] [1oqd_N] [1oqd_J] [1oqd_A] [1oqd_E] [1oqd_O] [1oqd_D] [1oqd_G]
  • SWISS-PROT database: [Q9Y275] [Q02223]
  • Domain organization of [TN13B_HUMAN] [TNR17_HUMAN] by SWISSPFAM
  • Domain found in 1OQD: [TNF ] by SMART
  • Other resources with information on 1OQD
  • Community annotation for 1OQD 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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