3MDY Transferase Isomerase date Mar 31, 2010
title Crystal Structure Of The Cytoplasmic Domain Of The Bone Morp Protein Receptor Type-1b (Bmpr1b) In Complex With Fkbp12 An 193189
authors A.Chaikuad, C.Sanvitale, P.Mahajan, N.Daga, C.Cooper, T.Krojer, I. S.Knapp, F.Von Delft, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C. A.Bullock, Structural Genomics Consortium (Sgc)
compound source
Molecule: Bone Morphogenetic Protein Receptor Type-1b
Chain: A, C
Fragment: Bmpr1b Cytoplasmic (Gs And Kinase) Domain (Residu 502);
Synonym: Bmpr1b, Bmp Type-1b Receptor, Bmpr-1b
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bmpr1b
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfb-Lic-Bse

Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Fkbp1a
Chain: B, D
Fragment: Fkbp12
Synonym: Fkbp12, Ppiase Fkbp1a, Fk506-Binding Protein 1a, F Rotamase, Immunophilin Fkbp12, 12 Kda Fk506-Binding Protein Fkbp, Fkbp-12;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fkbp12
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-R3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
65.410 80.010 183.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand LDN enzyme Transferase E.C. BRENDA
note 3MDY is a representative structure
D, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (303 Kb) [Save to disk]
  • Biological Unit Coordinates (3mdy.pdb1.gz) 150 Kb
  • Biological Unit Coordinates (3mdy.pdb2.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 3MDY
  • CSU: Contacts of Structural Units for 3MDY
  • Structure Factors (3109 Kb)
  • Retrieve 3MDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MDY from S2C, [Save to disk]
  • Re-refined 3mdy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MDY 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 3MDY
  • 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 3MDY, from MSDmotif at EBI
  • Fold representative 3mdy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mdy_A] [3mdy] [3mdy_D] [3mdy_C] [3mdy_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3MDY: [GS ] by SMART
  • Alignments of the sequence of 3MDY with the sequences similar proteins can be viewed for 3MDY'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 3MDY
  • Community annotation for 3MDY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • 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