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
  • 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
  • Domains found in 4DKD: [IG] [IGc2 ] by SMART
  • 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.

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