5VZ4 Signaling Protein Protein Binding date May 26, 2017
title Receptor-Growth Factor Crystal Structure At 2.20 Angstrom Re
authors D.Lakshminarasimhan, A.White, R.K.Suto
compound source
Molecule: Growthdifferentiation Factor 15
Chain: A
Fragment: Unp Residues 197-308
Synonym: Gdf-15, Macrophage Inhibitory Cytokine 1, Mic-1, N Activated Gene 1 Protein, Nag-1, Nsaid-Regulated Gene 1 Pro 1, Placental Tgf-Beta, Placental Bone Morphogenetic Protein Differentiation Factor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gdf15, Mic1, Pdf, Plab, Ptgfb
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Expi293f

Molecule: Gdnf Family Receptor Alpha-Like
Chain: B
Fragment: Unp Residues 115-351
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gfral, C6orf144, Unq9356pro34128
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
symmetry Space Group: I 2 2 2
R_factor 0.191 R_Free 0.254
length a length b length c angle alpha angle beta angle gamma
75.352 88.768 121.293 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BR, EDO, SO4 enzyme


Primary referenceNon-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15., Hsu JY, Crawley S, Chen M, Ayupova DA, Lindhout DA, Higbee J, Kutach A, Joo W, Gao Z, Fu D, To C, Mondal K, Li B, Kekatpure A, Wang M, Laird T, Horner G, Chan J, McEntee M, Lopez M, Lakshminarasimhan D, White A, Wang SP, Yao J, Yie J, Matern H, Solloway M, Haldankar R, Parsons T, Tang J, Shen WD, Alice Chen Y, Tian H, Allan BB, Nature. 2017 Sep 27. doi: 10.1038/nature24042. PMID:28953886
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (5vz4.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 5VZ4
  • CSU: Contacts of Structural Units for 5VZ4
  • Structure Factors (314 Kb)
  • Retrieve 5VZ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VZ4 from S2C, [Save to disk]
  • View 5VZ4 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 5VZ4
  • 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
  • Fold representative 5vz4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vz4_A] [5vz4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VZ4
  • Community annotation for 5VZ4 at PDBWiki (http://pdbwiki.org)

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