5VT2 Signaling Protein date May 15, 2017
title Crystal Structure Of Growth Differentiation Factor
authors X.Min, Z.Wang
compound source
Molecule: Growthdifferentiation Factor 15
Chain: A, B
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: Escherichia Coli Bl21
Expression_system_taxid: 511693
symmetry Space Group: P 31 2 1
R_factor 0.207 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
64.720 64.720 172.530 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand EDO enzyme
A, B

Primary referenceLong-acting MIC-1/GDF15 molecules to treat obesity: Evidence from mice to monkeys., Xiong Y, Walker K, Min X, Hale C, Tran T, Komorowski R, Yang J, Davda J, Nuanmanee N, Kemp D, Wang X, Liu H, Miller S, Lee KJ, Wang Z, Veniant MM, Sci Transl Med. 2017 Oct 18;9(412). pii: eaan8732. doi:, 10.1126/scitranslmed.aan8732. PMID:29046435
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (5vt2.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 5VT2
  • CSU: Contacts of Structural Units for 5VT2
  • Structure Factors (907 Kb)
  • Retrieve 5VT2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VT2 from S2C, [Save to disk]
  • View 5VT2 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 5VT2
  • 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 5vt2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vt2_B] [5vt2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VT2
  • Community annotation for 5VT2 at PDBWiki (http://pdbwiki.org)

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