2Q1M Signaling Protein date May 24, 2007
title Crystal Structure Of Human Gitrl
authors K.Chattopadhyay, U.A.Ramagopal, S.G.Nathenson, S.C.Almo
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A
Fragment: Extracellular, Tnf Homology Domain
Synonym: Glucocorticoid-Induced Tnf-Related Ligand, Hgitrl, Activation-Inducible Tnf-Related Ligand, Aitrl;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfsf18, Aitrl, Gitrl, Tl6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3) Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-14b
symmetry Space Group: P 63
R_factor 0.215 R_Free 0.257
length a length b length c angle alpha angle beta angle gamma
72.691 72.691 53.101 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
Primary referenceAssembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function., Chattopadhyay K, Ramagopal UA, Mukhopadhaya A, Malashkevich VN, Dilorenzo TP, Brenowitz M, Nathenson SG, Almo SC, Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19452-7. Epub 2007 Nov 26. PMID:18040044
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (25 Kb) [Save to disk]
  • Biological Unit Coordinates (2q1m.pdb1.gz) 60 Kb
  • CSU: Contacts of Structural Units for 2Q1M
  • Likely Quarternary Molecular Structure file(s) for 2Q1M
  • Structure Factors (111 Kb)
  • Retrieve 2Q1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Q1M from S2C, [Save to disk]
  • Re-refined 2q1m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Q1M 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 2Q1M
  • 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 2Q1M, from MSDmotif at EBI
  • Fold representative 2q1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2q1m_A] [2q1m]
  • SWISS-PROT database: [Q9UNG2]
  • Domain organization of [TNF18_HUMAN] by SWISSPFAM
  • Other resources with information on 2Q1M
  • Community annotation for 2Q1M 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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