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 Diffraction	resolution	3.00 Å
ligand	BMA, NAG	enzyme	Transferase E.C.2.7.10.1 BRENDA
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 4DKD

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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_B] [4dkd_C] 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)

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