2QKQ Transferase date Jul 11, 2007
title Structure Of The Sam Domain Of Human Ephrin Type-B Receptor
authors J.R.Walker, D.Cuerrier, C.Butler-Cole, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc)
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A, B
Fragment: Sam (Sterile Alpha Motif) Domain
Synonym: Tyrosine-Protein Kinase Receptor Htk, Tyrosine- Protein Kinase Tyro11;
Ec: 2.7.10.1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ephb4, Htk, Tyro11
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 42
R_factor 0.220 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.566 73.566 25.679 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CL enzyme Transferase E.C.2.7.10.1 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (2qkq.pdb1.gz) 21 Kb
  • Biological Unit Coordinates (2qkq.pdb2.gz) 21 Kb
  • LPC: Ligand-Protein Contacts for 2QKQ
  • CSU: Contacts of Structural Units for 2QKQ
  • Likely Quarternary Molecular Structure file(s) for 2QKQ
  • Structure Factors (125 Kb)
  • Retrieve 2QKQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QKQ from S2C, [Save to disk]
  • Re-refined 2qkq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2QKQ 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 2QKQ
  • 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 2QKQ, from MSDmotif at EBI
  • Fold representative 2qkq from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qkq_A] [2qkq_B]
  • SWISS-PROT database: [P54760]
  • Domain organization of [EPHB4_HUMAN] by SWISSPFAM
  • Domain found in 2QKQ: [SAM ] by SMART
  • Alignments of the sequence of 2QKQ with the sequences similar proteins can be viewed for 2QKQ's classification [EPHB4_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 [EPHB4_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2QKQ
  • Community annotation for 2QKQ 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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