4DKD Cytokine Transferase date Feb 03, 2012
title Crystal Structure Of Human Interleukin-34 Bound To Human Csf
authors X.Ma, J.F.Bazan, M.A.Starovasnik
compound source
Molecule: Interleukin-34
Chain: A, B
Fragment: Active Core, Unp Residues 21-193
Synonym: Il-34
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il34, C16orf77
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell_line: Tni Pro

Molecule: Macrophage Colony-Stimulating Factor 1 Receptor
Chain: C
Fragment: D1-D3, Unp Residues 20-299
Synonym: Csf-1 Receptor, Csf-1-R, Csf-1r, M-Csf-R, Proto-On Fms;
Ec: 2.7.10.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Csf1r, Fms
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_cell_line: Tni Pro
symmetry Space Group: P 31 2 1
R_factor 0.252 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.361 101.361 175.252 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand BMA, NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Basis for the Dual Recognition of Helical Cytokines IL-34 and CSF-1 by CSF-1R., Ma X, Lin WY, Chen Y, Stawicki S, Mukhyala K, Wu Y, Martin F, Bazan JF, Starovasnik MA, Structure. 2012 Apr 4;20(4):676-87. Epub 2012 Apr 3. PMID:22483114
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (4dkd.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 4DKD
  • CSU: Contacts of Structural Units for 4DKD
  • Structure Factors (276 Kb)
  • Retrieve 4DKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DKD from S2C, [Save to disk]
  • Re-refined 4dkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DKD 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 4DKD
  • 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 4DKD, from MSDmotif at EBI
  • Fold representative 4dkd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dkd_A] [4dkd_C] [4dkd] [4dkd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4DKD with the sequences similar proteins can be viewed for 4DKD's classification 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 at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4DKD
  • Community annotation for 4DKD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science