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 Diffraction	resolution	2.60 Å
related structures	by homologous chain: 1KD7, 1OQE, 1XU2
Gene Ontology	Chain Function Process Component F, E, C, A, J, B, H, D, I, G N, K, Q, M, L, O, P, R
Primary reference	Ligand-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

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 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] 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)

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